Leave chaff be, but limit NPC's to having the same amount of chaff as players, no unlimited number of materials to continue to synthesize it, and the same cooldown as everyone else.
NPC Chaff is one of the reasons I learned to love the Plasma Accelerator - you can't chaff plasma.
Something I would like though - Emissive Weapons: These raise a ships emissions. Why not make them a viable counter for Chaff? If a ship's emissions are raised enough reduce the effectiveness of chaff. Simple and effective.
Good suggestions
In no game ever is a hardcounter to any weapon system a "reasonaly balance"
missiles can overcrowd poit defense, and point defense has dead angles iirc. but a stupid doublechaff can just nullify one gimballed or even 100 gimballed wepaons. That is absolutely unreasonbly "balanced".
beign able to nullify gimballed is also a big reason for ship imbaalnce when their hardpoints aren't well distributed beause you need fixed wepaons to counter gimball nullifiers. And fixed weapons down't work on widespread hardpoints.
Starting from the end, working back.
My Cutter uses 1 gimbled, 6 fixed, My T-10 uses all fixed, as does my Clipper. Frags, Missiles, Mines all work really well on widespread hard points. Missiles being a hard counter to any small ship with double chaff.
Double chaff
only nullifies gimballed weapons, that's literally all it does. You could argue that a row of 6 PD's on someone who knows to FA off fly backwards, totally nullifies missiles and torps, but that would be all it could do.
Someone choosing to put all their defensive eggs in one basket deserves the bonus their scissors carry when going up against paper, of course when they come up against a rock, their double chaff is 100% nullified, whether it's against 100 fixed weapons or just 1. Pretty well balanced (in comparison to the poor balancing that plagues the game in general).
You can still hit your target, and your weapons can still do damage so it's not a hard counter. Get closer, un target and aim manually, use gimballed weapons with a short range and wide spread and suddenly chaff is unfairly underpowered.