Engineer gives two target locks, cluster is two attacks. Possible to shoot both locked ships? And if so does it just use up one TL or both?

Nothing in thw rules saying you can target 2 ships with one cluster missile.

You spend the target lock AND discard the card to attack your target twice. You can't split the targets.

You cannot have two target locks on the same target. Thus, you spend your target lock (that is on the target ship) in order to fire the torpedo/missile. The second target lock is on a different ship, and cannot apply to the current attack.