Why couldn't docking bays have fighters inside? NPC ones. Buy them like you buy any other ammo. All models already available for missions. Release them when in need of fighter cover, one by one or all together. Empty docking bays means that players can dock.
Best level of those NPC is something I couldn't guess. Maybe try with same equipment like players use - from AU8 to class9 guns. CD? Huh, idk... maybe... Maybe NPC bombers should have snac + CD. Like more expensive and effective cover "ammo".
Heavy carriers should be mean like... carriers. Atm they are just sitting ducks.