The fighter spawn really is just a fake ship. It's a very very small 3d model which you can barely see when zooming all the way in. It can't move and only has docking points for fighters. The fighters are more or less docking and undocking in the emptyness of space - I just spawn an animated subspace effect at the docking point's position to make it appear as if they're warping in.
All capital ships currently in the game can spawn fighters this way, so you don't actually need the fake ship for that. It really only serves two purposes:
1) allow for fighters or bombers to operate without the presence of a carrier ship (which isn't possible in vanilla Nexus)
2) the Nexus Skirmisher doesn't support adding fighters or bombers to a specific ship of your fleet, but I still wanted to give the player some control over what fighters and bombers he wants to bring along
Real fighter bays will be possible as well, of course, although it isn't implemented yet for any ship. The Moloch actually should, though, as it's supposed to have fighter bays (unlike the other cruisers and corvettes). Fighter bays will probably work with the help of some white-list of shipclasses... classes not on the list will spawn fighters via subspace (as they all do now) while ships on the list will have regular docking and undocking animations.
PS: Yeah, the subspace icon needs shrinking.
I literally created the icon in the last few minutes before actually uploading the mod... was using some placeholder beforehand, which was much smaller. Guess I just didn't think this through enough