I've thought about it for some time - even for how much this game is a sandbox, it does treat some matters rather seriously. One notable thing it doesn't treat seriously though, is ship construction. You can start with a flying container and, through expenditure of time, just manually weld bits and pieces on until it's a luxury yacht, megafreighter, space cruiser, whatever.
That doesn't quite seem... serious enough. Also shipbreaking is nominally a focus of the game, but ships are nothing but thin metal shells with components bolted on.
My proposed change is fundamental, but simple. Each ship model out there, gets a unique construction layer that the player can't easily modify or repair. A "structure" layer, essentially, with two types of tiles. The "frame", and the "hull". The frame is the fundamental base of the ship, that keeps the entire rest of the ship together and determines its shape. Certain things can only be built on or adjacent to the frame of the ship, things like airlocks, reactors, thrusters, anything with high mass or exerting large forces on the ship. Some things can't be built on frame tiles - things like storage bays built into floors, the center reactor tile that houses the torch drive (meaning the reactor needs very specific placement). The hull of the ship, is the "floor" of the structure. It defines the actual build area of the ship, and actually holds pressure. A ship with intact frame and hull but no floor tiles will have atmosphere, but no walkable surfaces. Hull can be built adjacent to, for patching purposes. However, patches are not hull - large enough holes in the hull can't be patched with just floor tiles.
Ships with hull damage can be theoretically repaired by hand. Repairing the hull is difficult and time-consuming, but possible. Damage to the frame is basically permanent, unless some manner of shipyard exists. Thus the boneyard around Ganymed, where ships too damaged for easy repairs are gathered.