Yeah I've thought this would be a good idea for a while...
But how about instead of each ship has several loadouts, you have just a selection of loadouts that you can add to and delete from, and each loadout has a ship assigned to it however you choose. The current default loadouts (one for each ship) would be there by default, but if you could change or delete them as needed. That way, if you really wanted 10 different galleon loadouts and no other ships, you could.