Without looking into the files I'd say Corvette, Frigate, Capital, SuperCapital and StaticObject.
I'm not a 100% sure but the layer doesn't primarily determine the altitute of a ship. If two objects share the same layer, from the pathfinding perspective they might collide and so will evade each other. It's therefore more of a tag for pathfinding.
The height of a ship can be set by <Layer_Z_Adjust>, no matter what layer a ship uses. If any...
Yeah, I got one. How long ago did you play those games? Because for my part it's been awhile and I'd forgotten about the TIEs vulnerability,,,
Half a live, I think. But it was one of my first games (and the very first I modded) and I loved it.
And if I reflected about it, I probably could recap most of the missions.
By law of physics EMP cannot work in space. Inside ship with atmosphere yes, but EMP in vacuum of space doesn't work - no air (or any other kind of atmosphere for that matter) no carrier for EMP blast, so technically certain locations on outer shell of the ship are 100% immune to ion bolts.
You don't need a medium to transport electromagnetic waves or to sustain electromagnetic fields. At least in our universe.