Missiles track now. That is a major improvement and really really nice.
Now they ofc need to be balanced to fit in.
I think they should be support weapons, not "spam and win" like now. At the moment, there is no way you can beat these ships and there is no need to use guns at all.
My suggestion:
Refire: Reduced. Maximum should be 1 missile / second or even 1 missile / 2 seconds
Damage: Reduced. They just take too much hull/shields for a weapon that hits a lot.
In general, it is damn cool to see missiles work now.
It will need some adjusting, but making them work is awesome.