Iíve been asking this question ever since the game launched and I have yet to ever get an answer to it.
The Technology to make Carrier support craft upgradable would seem to already exist in-game has evident with our Captains, Bridge Officers and our Vessels.
The customization options for Deployables could be limited to Weapons, Shields and Engines (sort of like the item upgrade system that they use in the MMO from a galaxy far, far away)
You want more shield cracking, then outfit your ToDuj or BOP with Tetryon cannons.
You want more punch with your Torpedoís, then swap out the fighters Photons for Quantumís.
I know that many others Carrier Captains feel that just having more rarities of existing Hanger Support Craft (I hate the term pets) would be more than enough and they might be right; however, I personally would like to have more say in what equipment is use by the things that my Carriers can Deploy.