They should have Tyranid miasma as the equivalent of PS2's death zones. This way your character suffocates in a way that doesn't break the lore or your immersion.
The Armed forces of the United States have had aerial insertion for years, and still have swim qualifications. One example, I know real world, does not apply to game world (always) but in this case I think it debunks one of your arguments. I would say it is not a big deal since, as you pointed out, if armor can be sealed well enough to survive in space, it is going to be good for most water work one would have to do. I am a bit surprised that the lore and fluff don't touch on it more.
Yes they can (without armour of course) the Iron Snakes hunt wyrms in the oceans of Ithaka with just a thong (lol) and a spear.
