Kroom Missile Factories on fighters are already kind of meh due to labor requirements. Making them any bigger would make them useless on capital ships even if you didn't mind breaking all vanilla designs.
I don't think you'll be able to get Cannon Factories off of fighters except by making cannons obsolete with an energy weapon that starts fires. An auto-feeding storage might help, but would probably get more use buffering guns on capital ships while fighters still used factories.
Fighter nukes are probably unavoidably overpowered. Torpedoes fill the same niche and are already quite strong. I'm not sure about EMP. I don't think I'd use them because it would require redesigning all of my carriers to fit a EMP factory, though they'd be useful against enemies with thorough vanilla shield coverage.
I've tried to make factories on fighters work because torpedoes are very good, but the closest I've gotten is this:

And it just doesn't work. The torpedoes give great burst damage against unarmored components, but the sustained damage to cut through the armor first just isn't there. I've done better with a bunch of tachyon guns for cutting through armor and one or two torpedoes for making a mess inside and the tachyon guns just don't fit with a missile factory in the 9x9 square that actually fits nicely on a landing pad.
Well, that's not entirely true. I've found this makes a good fire support ship early on, but while it's a fighter in that it fits on a landing pad and has no FTL of its own, it uses full size missile launchers because its job requires the range.

The only place I'm really happy with fighter scale missile launchers fed directly by a factory is on smallish starships that are just a bit too narrow to have two turrets, leaving an otherwise useless empty spot that can be made 3x5 by moving some crew quarters around. And that's not because they're good, but because they're anything remotely useful that fits.
If fighter missile launchers were made to only reload from teleporters and landing pads it would wreck a bunch of my starships but no fighters that aren't already failures. If that could only be done by removing the doors it would also wreck a bunch of my fighters that don't have a factory, but do require crew to climb over missiles or torpedoes to reach some of the engines.