Ever consider the balance of missiles is fine and it is something else at fault instead?
In comparison to other weapons in the game that you can fit on the same slot, missiles are weak.
Missiles as they stand are probably powerful enough, overall the problem with balance in general is that it is all about trade offs. It does not matter if the opposition is PC or NPC, the concerns with balance are the same in essence.
Gimballed Multicannons -> Do decent damage to shields, fire 90 shots in a row, track enemy target, can be fit on C1 and C2 weapon slots, deal decent damage to hull, you get ~2000 shots total, ammo is inexpensive, and they produce very very very little heat, meaning you can keep 1-2 pips in weapons and fire them non-stop.
Heat Seeking Missiles -> Do virtually no damage to shields, have a limit of about 30(?) ammo, can be fit to C1 and C2 weapon slots, track enemy target, do mediocre damage to hull, ammo is expensive, they produce a lot of heat, they require a lock on period.
Why would anyone use missiles when gimballed multicannons outperform them? This is the very definition of balance. Try this.. Go get a viper, and equip it with C1 and C2 heat seeking missiles. Get a friend to outfit a ship however he wants. Attempt to destroy him with missiles. Then get the same friend in the same ship to go against your Viper with C1 Multi's and C2 Multi's, and do the same thing. Tell me which is better.
The only difference really is that certain types of player opponents tend to min-max/meta which may result in certain weapons becoming less effective against them. Perhaps it is the min-max/metas that need to be nerfed as opposed to weapons beefed up.
The last sentence here makes absolutely no sense. You can't nerf people min/maxing. You can't remove min/maxing from a game unless you make everything the exact same. Clearly you don't know what the word "META" means.