I always thought they were dead in battle. The Borg didn't believe in assimilating lifeforms until "Best of Both Worlds." Yet others argue they were assimilated, and hence they were into assimilation the whole time.
The concept of assimilation was introduced in Best of Both Worlds, but later works develop the concept and even retcon it as the modus operandi of the Borg.
The Voyager episode Raven, in particular, shows how 7 of 9 was assimilated years before the events of Q Who.
As for Guinan not mentioning it - we see multiple times where assimilation is treated as efffectively death - even despite the recovery of individuals such as Picard, so perhaps she just didn't see the point of specifically mentioning it.
So, the evidence points to the 18 crew members either dying from decompression or being assimilated. As has been discussed, EU novels indicate assimilation, but the TV shows and movies are silent on this matter. Either way, they would have been listed as simply missing, presumed dead.
It was revealed in the EU novel Greater than the Sum that the eighteen crew members were in fact assimilated by the Borg, rather than killed by exposure to space (or sliced in half by the Borg cutting beam), as the episode would seem to suggest.
“I’m sorry, have we met before?”
“Of course, you wouldn’t recognize me, not like this…” She came to attention. “Lieutenant Rebekah Grabowski, sir. I was a member of your crew aboard the Enterprise-D for nearly two years…until I was taken.”
Picard’s jaw dropped. He recognized the name. He remembered all their names, even after fifteen years. “Rebekah Grabowski. You were…one of the eighteen. The first eighteen people we ever lost to the Borg.”
“It was difficult for us to function at first,” Hugh told the senior staff as they sat around the table in the observation lounge. The ex-drone-leader of the Liberated, as he called them-had come aboard along with Rebekah Grabowski, who still looked amazed and delighted to be on a Starfleet ship again, even a different Enterprise from the one she’d known. Picard was equally amazed to have her back. He still remembered the day the Borg had carved a cylindrical section out of the ship like a core sample, taking her and seventeen others with it. At the time, he had not known of assimilation and had believed them to have been killed, discarded by a race that, according to Q, had been interested only in technology (more proof, in retrospect, that Q was not a reliable source of information). After his experience as Locutus, he had wondered if perhaps they had survived as drones instead, and prayed that they had not.
The evidence is inconclusive.
In "Q Who" there was no evidence that the Borg assimilated any biological beings into their collective. So presumably the Borg would probably have killed any Enterprise crew or passengers that survived the decompression when a section of the Enterprise was sliced off and seized by the Borg.
But there is no proof that the Borg did kill them. It is possible that the Borg assimilated them, or dropped them off on a habitable planet, or did something else that didn't kill them.
In "The Best of Both Worlds" the Borg assimilated one lifeform that we know of, Picard, for the special purpose of serving as a spokesdrone for the Collective during the conquest of the Earth and/or the entire Federation. Picard's message offered some hope of survival for other Earth people/Federation citizens:
PICARD [on viewscreen]: I am Locutus of Borg. Resistance is futile. Your life as it has been is over. From this time forward, you will service us.
This offered some hope that some Earth people/Federation citizens would survive and live as workers for the Borg as employees, serfs, slaves - or possibly farm animals harvested for spare organs for Borg drones needing transplants.
Of course Locutus could have been lying to reduce resistance and the actual plan of the Borg could have been extermination.
Did the Borg assimilate anybody else during their invasion of the Federation?
At the beginning of "The Best of Both Worlds Part 1" the Enterprise investigates the disappearance of the New Providence colony on the distant planet Jouret IV.
RIKER: Mister O'Brien>
RIKER [OC]: Verify these are accurate coordinates for New Providence colony.
O'BRIEN: Coordinates verified, sir.
O'BRIEN [OC]: You're at the centre of town. (The centre of town is at the edge of a massive crater)
They later search for traces of Borg energy in the soil to verify it was a Borg attack.
There is absolutely no mention of getting information from survivors of the attack. So all of the colonists - men, women, and children - were either killed or captured and assimilated by the Borg. And there is no information whether the colonists were 100 percent killed and 0 percent assimilated, or 0 percent killed and 100 percent assimilated, or anywhere in between.
In "The Best of Both Worlds Part 2" the Enterprise arrives at the site of the battle of Wolf 359 between "forty" starships and the invading Borg Cube.
WESLEY: We're approaching the Wolf system, Captain.
RIKER: On my way.
RIKER: Slow to impulse. Take us to the battle coordinates, Mister Crusher. Yellow alert.
WORF: Sensors are picking up several vessels, Captain.
RIKER: The fleet?
DATA: No active subspace fields. Negligible power readings.
RIKER: Life signs?
DATA: Negative, sir.
WORF: Visual contact.
RIKER: On screen.
(Fragments of starships, some with flashes of fires still burning)
SHELBY: The Tolstoy, the Kyushu, the Melbourne.
(Riker bows his head briefly for the crew that might have been his)
So all the starships that did not successfully retreat from the battle have been smashed.
All crew members who didn't escape from the ships that were smashed by the Borg are dead, or else have been captured and assimilated and are now on the Borg cube.
Tens, hundreds, or thousands of crew members may have escaped from smashed ships in shuttles and lifeboats.
All of those tens, hundreds, or thousands of crew members have either escaped beyond range of the sensors of the Enterprise, been killed by the Borg, or been captured by the Borg and assimilated. The last group would now be on the Borg cube.
The Borg cube explodes at the end of "The Best of Both Worlds Part 2". That presumably kills all lifeforms inside it, including everyone who might have been assimilated at New providence or Wolf 359.
In "The Drumhead" retired Admiral Norah Satie questions Picard:
SATIE: Tell me, Captain, have you completely recovered from your experience with the Borg?
PICARD: Yes, I have completely recovered.
SATIE: It must have been awful for you, actually becoming one of them, being forced to use your vast knowledge of Starfleet operations to aid the Borg. Just how many of our ships were lost? Thirty nine? And a loss of life, I believe, measured at nearly eleven thousand. One wonders how you can sleep at night, having caused so much destruction. I question your actions, Captain. I question your choices. I question your loyalty.
Admiral Hansen said that "forty" ships were gathered at Wolf 359 to fight the Borg. Satie said that thirty nine were were lost. So possibly there were only thirty nine ships at Wolf 359, and all thirty nine ships were destroyed. Or possibly Satie was wrong and there were forty ships at Wolf 359 and all forty were destroyed - though it would have been odd for her to understate the destruction she accused Picard of causing. Or possibly there were forty or more ships at Wolf 359 and one or more ships escaped.
The Enterprise NCC-1701 D usually had about a thousand people aboard. If all thirty nine ships at Wolf 359 had that many people aboard, that would make a total of about thirty nine thousand.
About thirty nine thousand (or about 38,000 to 40,000) minus almost eleven thousand (or about 10,500 to 11,000) makes a difference of about 27,000 to 29,500 persons.
Maybe the difference is that most of the ships at Wolf 359 had much smaller crews than the Enterprise NCC-1701 D did. 10,500 to 11,000 divided by 39 is 269.23076 to 282.05128, so we might imagine that the typical ship at Wolf 359 had about 250 to 300 people aboard and everyone was killed.
Maybe the difference is that most of the ships at Wolf 359 left most or all of their non combat essential crew and all their passengers at planets or starbases, etc., before reaching Wolf 359 for the battle and so had much fewer people aboard than the Enterprise NCC-1701 D did.
Maybe tens, or hundreds, or thousands, or possibly tens of thousands, of crew members escaped from the Battle of Wolf 359 and were confirmed to be alive and well in the months before "The Drumhead".
Maybe Satie drastically understated the number of deaths at Wolf 359 - though it would have been odd of her to understate the deaths she accused Picard of causing. Possibly the official death count only listed those crew members whose DNA had been identified in body parts found at Wolf 359, and all the thousands of other crew members were listed as "missing, presumed dead". But it would have been odd of Satie to exclude the "missing, presumed dead" from her count of the deaths she accused Picard of causing.
Maybe some combination of all four factors explains the 27,000 to 29,500 person difference in fatalities at Wolf 359.
So far there is no proof that the Borg assimilated any Federation citizen except for Picard, and no proof that they did not assimilate thousands of Federation citizens.
Yeas later, "Emissary", the first episode of star Trek: Deep Space NIne, opened with a flashback to the Saratoga at the Battle of Wolf 359. The Saratoga is wrecked, and Benjamin Sisko's wife Jennifer is killed, but at least one escape pod escapes before the Saratoga explodes. Those aboard the escape pod include Benjamin Sisko and his young son Jake.
And some fans have wondered how it was possible for this escape pod, and any others, to travel so far before the Enterprise arrived at the battle site that the scanners detected no life. Could Ben and Jake Sisko survive?
Whether nor not Ben and Jake Sisko actually survived, three years later people who were accepted as Ben and Jake Sisko arrived at Deep Space Nine, where the alleged Commander Benjamin Sisko reported for duty and became the Starfleet commanding officer and the protagonist for all seven seasons of the show.
In the television series Branded (1965-66) the protagonist Jason McCord was discharged from the US army for allegedly deserting his post at the (fictional) Battle of Bitter Creek, and became known as "the Coward of Bitter Creek".
All but one man died.
There at Bitter Creek.
And they say he ran away...
And if Ben, Jake, and the others in their escape pod were the only survivors of the Battle of Wolf 359, they might have been suspected of desertion, or possibly of being captured and brainwashed by the Borg and serving as Borg spies. Possibly Ben Sisko would have been discharged from Starfleet and called "the Coward of Wolf 359".
So it seems likely to me that a bunch of other shuttlecraft, escape pods, and lifeboats escaped from the starships at Wolf 359, carrying tens, hundreds, thousands, or possibly tens of thousands to persons to safety. Then people would probably either suspect all of the surviors of being cowards or Borg agents, or suspect none of them. So Ben Sisko would probably have continued his Starfleet career normally without being called "the Coward of Wolf 359" or (especially) suspected of being some sort of spy.
But this is just speculation on my part. There is no evidence that anyone escaped from Wolf 359 except for Ben, Jake, and anyone else seen in their escape pod. And there is no proof that Ben, Jake, and anyone else seen in their escape pod actually survived and escaped. It is possible that some group, such as the Borg, Species 8472, or the Sphere Builders in Star Trek: Enterprise sent duplicates of persons killed at Wolf 359 to pretend to escape from Wolf 359 and spy upon the Federation.
Years later, in Star Trek: First Contact the Borg ship that travels back into Earth's past has a policy of assimilating every human possible, injecting nanoprobes to turn them into Borg.
So did the Borg change their policy between "Q Who" and "The Best of Both Worlds" or between "The Best of Both Worlds" and Star Trek: First Contact?
Or did different ships and groups of Borg have different policies in "Q Who", "The Best of Both Worlds", and Star Trek: First Contact?
Or did all Borg have the same policy everywhere during "Q Who", "The Best of Both Worlds", and Star Trek: First Contact, but it was a complicated policy mandating extermination in some circumstances and assimilation in other circumstances?
I have read that some of the Borg in Star Trek: First Contact looked liked that members of such local species as Klingons, Romulans, and Vulcans - I never noticed that myself. If so they would have been assimilated by the Borg in previous battles or invasions, or from among the Enterprise crew earlier in the movie.
And I have heard that some Borg encountered in Star Trek: Voyager in the Delta Quadrant were allegedly Starfleet crew members captured and assimilated at Wolf 359. If so, how did they survive the explosion of the Borg Cube?
Presumably the Borg cube could have sent a smaller ship contained within it back to the Delta Quadrant through a Borg transwarp conduit, and some of the people assimilated at Wolf 359 could have been among the drones in that ship sent to the Delta Quadrant.
So therefore, it is possible that the Borg began assimilating a lot of Humans and Federation citizens as early as "The Best of Both Worlds", and possibly as early as "Q Who".
But the available evidence is totally inconclusive about the fate of the 18 crew members in "Q Who".