I have the impression that no matter how many PDC you have on a ship you can't shoot down more than one missile at the same time. I observed that with my ship as target but also when I attacked a starbase: when I fire two missiles at the same time one of them always did hit the starbase in spite of its 4 PDC.
Is this correct? If so I would consider it a bug.
The PDCs will fire on the nearest threat until it is destroyed.
But they also have a small delay between one cannon firing and the next.
If you put enough cannons on, you can get a continuous stream of PDC fire, and knock out lots of missiles.