Foreword: Tnx for making missiles work! The last version really was a disappointment when missiles would sometimes track, and mostly not. Having tracking missiles that hit and do damage and add to pvp is a real technical breakthrough.
Now to balancing:
Blodo has mentioned most necessary points already. So I only add some ideas of mine that I gathered from brutally spammy LF vs. LF fighting
Passive counterstrategy imo could be: "shields do well against missiles".
I was fighting with Firestalkers and Sidewinders and they both were so damn lethal because they were so effective against shields and hull.
If missiles (except the anti shield missiles) did good hull damage, but were not very useful against shield, you'd get the Hellfire tradeoff: "you need guns/mines to down shields => then you can missile the hull".
This would also reintroduce strategy and skill into the game and would give guns a reason to be used (kind of hard atm because the missing shieldbubble makes gunning so much harder).
Active Counter: CMs do work already if you drop them manually. It's however very difficult because of the missile spamminess (especially the insane refire of Firestalkers!). If missiles refire more slowly, CMing them with skill and evasive turns would already work. But CMing 5 incoming missiles via well-timed CMs and maneuvers at the same time ofc cannot work.
Generally, I think missiles should find their role in pvp; EMP to down shields, MR+Codes for shotgunning, missiles for hull damage on deshielded snubs, e.g. in chase fighting (when target is on full-dodge and nearly unhittable with anything else). They should however not be the solution to everything.
How fast should missiles be fired?
Max speed: 1 missile / 1 second.
Likely better: 1 missile / 2 seconds
A typical joust-turning pvp match should not allow any side to fire more than 2-3 missiles per approach (perhaps excluding low damage almost-Hellfire-type) missiles.
Hope that helps.
I'll take the other named categories into account when I go and test again.