Babylon 5 creator J. Michael Straczynski was very active online during the shows's run, and addressed many of these questions. Even from the earliest days, he acknowledged that security was a problem, and would cause issues on the station.
Lots of people and lots of stuff coming and going means inevitably, things are going to slip through
There is a security problem on B5, yes. And we hope to deal with it
at some point. It's inevitable, really; 250,000 residents, huge crates
being moved in and out every day, people going and coming...they try to
confiscate what they can, but a lot slips through. (Usenet 3/23/1994)
As JMS points out, security is hard when you've got that many people and that much stuff, and inevitably something is going to slip through. Even in our modern day, this is a problem. In 2015, the United States' Transport Security Administration (TSA) had a 95% failure rate for letting dangerous objects through during undercover tests. Babylon 5 is doing pretty well actually given how few incidents there were over five years.
Confiscating weapons smuggled by diplomats will likely cause a diplomatic incident
A prominent example we see of this is when Londo Mollari assembled a hidden weapon in Midnight on the Firing Line in an attempt to murder G'Kar. JMS notes that pretty much all of the ambassadors have smuggled in weapons via diplomatic pouches and confiscating them could lead to a diplomatic incident.
My thought, at the time, was that if we play the reality of this for a
moment, probably *all* of the ambassadors have some kind of weapon, smuggled
in via diplomatic pouches. Garibaldi and Sinclair know they're
there...question is, is it worth starting a diplomatic incident over, as long
as they're not being used? Garibaldi is saying, in essence, "Okay, you know
it's there, and I know it's there, but now you've made a point about it. Lose
it or hide it, or I'm going to have to charge you, and we're BOTH going to be
up to our ears in it." If Garibaldi confiscated it, there'd be a whole
diplomatic hassle...and Londo would just have another one sent to him via
diplomatic pouch. (GENIE 1/23/1994)
Note too that Babylon 5 security, before breaking away from Earth, was a regulated part of Earthforce military. After they broke away, many Narns joined the security force. Having a human kick down the Minbari ambassador's door, or a Narn kick down the Centauri ambassador's door, is just asking for trouble. Given that Babylon 5 is the "last, best hope for peace" between many enemy races, they would rather not risk this so long as they are not actually using the weapons.
A known fixer on the ship is better than one who is unknown
Although he primarily does forgeries and stuff, some weapons appear to be available from N'Grath, who was a fixer on board the ship throughout Season 1.
Garibaldi is quite aware of n'grath...and knowing that if he just
vanished, somebody'd take his place in five minutes, prefers the trouble
he knows to the trouble he'd have to track down.(Usenet 2/18/1994)
Ironically, he did disappear, although that was because JMS felt he didn't work out as well as intended. Again, knowing who is supplying people is better than not knowing. Heck, Garibaldi even approached N'Grath himself when he was on the run, although he insisted he was just a "legitimate businessman."
The station is 5 miles long, and some areas are poorly monitored
Dr. Franklin went on walkabout for much of Season 3, and Babylon 5 staff had no idea where he was for most of it. While he didn't do anything wrong, I think this shows that keeping tabs on someone who might be a threat is next to impossible if they are hanging out in relatively unmonitored sections of the station, like Brown Sector.
JMS notes that there are places that are less monitored by security, like an air lock in the zero-g section where a body was dumped out in And the Sky Full of Stars.
Yes, it was always my assumption that the body was dumped out through
the zero-g section, since that has more traffic with cargo loaders and
unloaders and less security than the passenger-oriented bays and airlocks. (Usenet 3/23/1994)
Even if there were security cameras in places like these, Babylon 5 security can't monitor every inch of the place all the time, so they can't necessarily provide a timely response when incidents like this occur. Plus, it's easy enough to disguise yourself during this.
Sheridan acknowledges that someone trading their life can't easily be stopped by security
Since many of the things on your list are assassination attempts, I'd like to point out an exchange from Season 5's No Compromises in which an assassin threatened to murder Sheridan at his inauguration.
Sheridan: I can't go along with postponing the ceremony.
Garibaldi: Just for a few days until we can bring in more security. Now whoever this guy is, we know he's killed one person already. The message he sent you is untraceable, that tells me he knows our system inside and out. He's smart, he's deadly, he's after you. That's good enough for me. [...]
Sheridan: Our new friend just said "All the security in the world can't stop a loan gunman dedicated to exchange his life for the target." And he is right. So you may as well live instead of being a prisoner.
Presumably, he had some of this attitude in previous seasons as well when he was in charge of the station. If someone really wanted to trade their life, security can do all they can to stop it, but ultimately, they have limits on what they can do.
Regarding the missing Grey 17…
I don't really see this as much of a security issue. The station schematics did not show a missing sector, and until Garibaldi started timing the elevator ride (because he was bored, mind you), nobody even suspected that there was a missing sector. After all, there was an official Grey 17 level.
Recall too that Grey Sector had a reputation for being the "B5 Triangle" with lots of unexplained occurrences. Say that someone goes missing in Grey Sector. Security searches, finds no clues, and eventually has to let the case rest. You can have all the security officers in the world, but it won't change a situation like that.