Well it is kinda understandable, that on a space ship there is limited number of crew quarters. But that those crew quarters vanish if you decide to build something else is from my opinion just a dick move. With that you either encourage the cheat or that you neglect the whole space fight part because your ship is full with advanced crewquarters.
Well, the space fighting part isn't finished, and if it is, it's not used a lot yet, so we can always neglect it as of now.
But i also understand why ship parts can take up some of your space, it's stupid but logical, you want to have a new generator, you install it where you can, if it's for a ship, it's likely to be big (or big enough) so it takes room.
Same thing for weapons, even if it's technically installed on the ship, there has to be parts inside, even if it's not talked about yet (because fenco can be lazy), weapons can be use by crewmates (and should be) so there is equipment inside your ship to be able to use the weapons, and it's likely there is ammunition (for ballistic weapons), charging batteries (for energy weapon) and maybe maintenance tools taking space as well.
Like i said, it's stupid, but it's logical to think that when you install something it's not "not taking space by magic".
But even tho i say that, i agree that it's a dick move, there is a "weapon space" and a "systems space" and it shouldn't take up crew space, the ship system is far from well made.
i just remember while i was checking for errors that the system had a lot of problems while it was being made and it stopped fenco from going to zeng-shi, so it's probably rushed af and most likely a placeholder (i hope).