I am running Redline and he can have 2 target locks on one ship. So if he shoots assault missiles or proton torpedoes he spends one of the target locks. Can he still use the other target lock to reroll any dice from that secondary weapon?

Yes! The first target when spent allows you to fire the missile/torp. The second Target lock allows you to modify the attack. In this case you are not using two target locks on the same attack.

Yep, that's the whole point of Redline's ability. Just don't use him with Homing Missiles.