The location of objects in cosmoteer is actually vital. Ammo factories and reactors need to be near guns or they won't fire often. Engines are physics based. If you don't armour your ship well or space things out you'll get a cascade explosion.
But the lack of 3d is a hard one to solve from a game design standpoint. It's hard to build an intricate 3D object using a 2D monitor and they are more complex to visualize and change.
Oh absolutely, not only technically but also because our brains suck at conceptualizing complex systems on a 3-D plane, the fewer the dimensions the more complexity we can handle - hence while a lot of circuitry diagrams are on either a 2-D or 1.5-D plane.
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.
But the lack of 3d is a hard one to solve from a game design standpoint. It's hard to build an intricate 3D object using a 2D monitor and they are more complex to visualize and change.