It should automatically target missiles, by proximity. You should have to manually fire them (press the button) but the nothing else should be required of you to get them to do their jobs.
But then I also suggested turning them into a psuedo flak-field defense, rather than a discrete-targeting weapon. You'd press the button and it would create an arc of small explosions (at a discrete distance) in the direction of your cursor. Drones and Missiles passing through this arc then take heavy damage or are destroyed. Flak batteries would then exist as on/off state weapons. While on, they continuously drain power (like cloaks), and then they have a moderate cooldown before they can be re-engaged again.
This arc of fire, while active, then remains firing in that direction relative to your ship till it gets switched off. This allows you to stack multiple flak batteries for larger coverage areas. For reference, I'm thinking +/- 45 degrees per arc, for a total of 4 required for full 360 degree coverage (4 medium component slots is a hell of a price to pay for an impenetrable missile defense...for as long as you've got power to sustain it).
I don't think that enemy ships should be able to fly through them with impunity, but the damage these flak batteries do to them should be rather minimal (1/4th or less of the normal damage).
Anyways, that was my idea for them.