I like the model! Just what I had in mind (though you ARE allowed to expand the sides or back if you like.) Having the launch tube there is great, it definitely implies more fighters back there. I can certainly imagine ships being guided out of storage onto the racks for weapon loadout and pilot assignment. Since you're doing the Hatshepsut hangar the same way (and this is, after all, your Colossus) it should be an excellent fit. A few more details to give it some human scale would be welcome; the elevator is a nice touch, but some catwalks, trapezoid doors, ceiling cranes, and lower level maintainence vehicles would complete the illusion.
Forget about having the AI fly into the hangar by themselves. They'll be using very precise paths for docking bay-based arrivals and departures.
The fighters in the hangar COULD be destroyable, nontargetable subobjects, if it were not for the subobject limit and additional table data required. As it stands they will be part of the hangar detail box and be indestructable.
