In Star Wars, everything is a Kalashnikov.

Anyway, in my over-excited way what I'm saying is if there's any setting ever in which it's justifiable that a spaceship should have such absurd fault tolerances that it could withstand multiple atmospheres of pressure, it's Star Wars. I have an adventure planned on a sunken ship. It's got flooded parts and air pockets and corroded killer droids and a mysterious killer and everything. It's going to be great. And your adventure should be too!

Very well put, Knass. I'm planning on the ships in question being Seppie ships: a Providence class and two or three Recusant class. The interesting thing about both of these is that they are Mon Cal and Quarren designs (Free Dac Volunteers Engineering Corps), which are designed to float on water if need be. So that's a bonus to my plot, but I do feel like despite the ruggedness of the setting you are rightfully suggesting, some modification to ships should be necessary.

Then add away! Especially if you want the ships to be functional underwater and able to take off out of it again like the spaceship at the end of The Abyss. (seriously hope that's not a spoiler for anyone - it's a very old movie). You might be able to lift an X-Wing out of a Dagobah swamp but that doesn't mean it could do it by itself. Quarren and Mon Cal ones however make sense that they could.

Meanwhile, elements of your story's plot sound a lot like mine. Although mine doesn't have a mysterious killer involved. Yet. I'm going to click "I would like to know more."

Well, to put it simply, you've seen Alien, right? Or maybe played Alien Isolation? It's going to be something like a cross between that and The Poseiden Adventure:

Much like yours, it's an old Seperatist capital ship, sunk beneath the waves. The difference from what I've gathered from your posts, is that this one is not salvageable. It's about survival, not rescue. And like all good horror films, the environment itself seems to align against you. Flooded passages, long, that the only way on is to hold your breath and swim through the dark; pockets of Tibana gas where everything must be powered down for fear of a fatal ignition ("but look where your team is - if they fire wont they rupture the cooling system?"); the creaking of thin metal that is the only thing that divides you from millions of tonnes of icy, black water. Any bulkhead you open could at any moment let in the ocean on you. Wrecked battledroids still man their stations, rusted and inert. The ship itself is angled, corridors are not level and occasionally slippery with intruding weeds and slime. And all the time, something is in there with you in the deeps. Something from the war, something cold and metal and which doesn't care about the pressure or the dark or the fouling air. But it can hear your footsteps echoing through the ship's structure, it can feel the heat in the floor where you have been and it absolutely will not stop until you are dead.

Good luck.