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In The Voyage Home, Kirk and crew spent so much time on past Earth only because of unavailability of a strong water tank. They even messed with the history which could be dangerous.
But, the question is: Why did they need a water tank in the first place? Whales are mammals which can breathe without water. Only their movements would have been compromised for a short time.
Without water, a zero-gravity environment would still have been dangerous for the whales.
In the absence of water, the whales would have needed null gravity within their chamber to keep from collapsing under their own weight. Without water to hold them in place, the whales would then have been vulnerable to buffeting. Even gentle maneuvering of the ship could drive two unsecured, multi-tonne squishy masses into the bulkheads, and the slingshot around the sun involved extreme acceleration and potentially violent maneuvering. As Star Trek has shown numerous times when bridge crews are thrown about, ships' inertial dampers can reliably cope with steady acceleration but not with sudden lurches.
Around the midpoint of the previous film, Enterprise attacks the same Klingon Bird-of-Prey. The Klingon bridge crew are jostled in their seats, and their reactions seem out of proportion to the bridge console explosions, which suggests that the entire ship is lurching:
In "Redemption, Part 1", a rebel Klingon vessel fires a torpedo at Gowron's flagship. The impact shakes Gowron (foreground, seated) and nearly knocks a standing bridge officer (background) to the deck. As the attack proceeds, the flagship continues to shake:
In The Voyage Home, Scotty undoubtedly could have cobbled together some sort of active restraint system using tractor beam emitters, but he was working with a limited supply of equipment and an unfamiliar programming interface. Water, as a passive restraint, was the safest option.
According to this website, whales need water to:
In short, it's because Kirk doesn't know how long their return journey will take. There's an extra piece of the dialogue (between Kirk and Scott) missing from the film that was apparently in the early shooting script and made it into the official novelisation
"Humpback whales. They're fifteen or sixteen meters in length. They'll mass about forty tons."
"They willna have much room to swim."
"It doesn't matter. They won't have to stay in the hold for long. I hope."
While Kirk is hoping they'll have a short uneventful trip back to the future he's anticipating the possibility that something will go wrong and they may end up spending more than a few hours with the whales in the hold, something that would be catastrophic for their health
Counterpoint, unsupported (as far as I know) by canon: It's for the acoustical properties.
One might recall that the whole point of kidnapping the whales in the first place was to get them to respond to an alien message.
Putting the whales into a water medium is important for both the whales' ability to hear and understand the message and for their ability to respond vocally.
As sensible as this seems to me and real-world physics, I don't think it has any actual canon support.
