Honestly, I think that drops from Threat fleets with fabricators should be, thematically speaking, based on just the fabricators. Give them some specific odds for dropping all of the various Threat things (weapons, hullmods, hullmod-enabling items), and just don't generate loot from the non-fabricator ships at all; thematically, those ships aren't special - they're just things the fabricators built before you got there.
Fleets with no fabricators should still drop loot based on the specific ships involved, of course.