I've played around a lot with missiles and I've found that they're quite weak when compared to cannons (cannons are definitely most powerful weapon type in the game).
The only success I've had with missiles is to put all my points into launchers and cloaking. Fill up all my available spots with torpedos (maybe 1 gravity missile). Put boosters in all none missile slots with the possible exception of drones, if you wish to pursue that tree. Get as many missile range/damage specialists as you can and then just barrage things from far away while holding the back button. If things get close, stop firing and run away.
If enough small ships or drones get in close enough, you'll have a very difficult time running away which can be problematic.
Against smaller ships, missiles are a better way to go as they rotate and track much better so you can constantly run away while firing, but they lack the power to punch through larger ships and stations, especially if they have point defense and/or zapper drones.
As for ship types, there's the volley for medium hulls, flora for large hulls, and carrier for huge hulls, though the star cruiser is alright as well.
If you are having trouble with zombies, try putting a laser into your turret and turn on turret auto firing. It works much better than PD for killing the zombie critters. Also, it helps if you never stop moving as you should be able to out run most of them. Zapper drones also target the critters.