pearl meteor
primary weapons use 6 for optimal firing / max firerate.
I think you could do it fairly similarly
Modules get set to having 6 max.
Secondary weapons get set to some sort of systems where they have 6 bullets and reload over time, or whatever should be applied to them.
I.E
you could have 8 rivets on a robot.
Then you have your choice of six modules - This is six, or if you stack them, that also adds to that number.
So two mass distortion modules = 1 slot for usage, but two of your module slots.
Having more of one module would improve either its use rate, what it does, or some combination of the two.
As for secondaries, You'd be able to put more than six, but like primary weapons they would only be able to use up to six at once. Secondaries would have a base very slow reload and a primary and secondary ammo pool probably that generates depending on the secondary. Also this would let you make secondaries that are actual weapons which at this point with how much people like missiles and autocannons could be desireable.
This would mean in respect to chaff and missiles:
Missiles get their amps most likely reduced, and you probably get a pool of 6 missiles with a reserve ammo dependent on how many total missiles you have. You'd have a speedy-ish reload from the reserve ammo, but a slow generation for the reserve ammo. Nano would also generate ammo.
Chaff would turn into a module you can only use every so often. Having more chaff increases the rate you can use chaff, maybe the health of the chaff cloud, etc. It'd be less cut and dry then chaff counters missiles.
Basically modules wont stack their effect like ammunition is the bottom line. This would let you improve the concusser, munitions forge (especially if its activated!!!!,), and you'd be able to make the turbo fuel injector feel reallly good with this manner of changes.
knotty spade
digital marlin