I agree, I think that we typically can't see "inside" so we need something 2D ... but people can handle 3D with the right visualisation. In our life experience, we tend to interact only with the surface of objects.
Bear in mind that circuit boards are actually 2.5D - they have up to 8 layers and have tracks inside, connected by either parts holes or "vias."
When it comes to diagrams, I think that is just because we use 2D paper, so we make 2d diagrams. If we had a nice 3D representation I think more people would use that.
Then again, it seems like overkill since you can split a circuit diagram into submodules: power supply, microcontroller, peripherals, ...
The difficulty in most spaceship games is that you create a "border" of hull, engines, etc. You then put in the "filler" for instance crew space, corridors, chairs, guns. What to do when you have so much "filler" that the "border" becomes too small? In Space Engineers I find this problem hard to solve as a player. It's less so in the 2D Cosmoteer.
