As confirmed by this ruling, the use of point defense against capital missiles is resolved on a per-missile basis. Using the same example, an AMS point defense bay engaging a bay of five white sharks fires five times, attacking each missile separately.
Somehow it only recently occurred to me to ask the followup question: What if the point defense can't? For example, Non-AMS point defense systems on large craft can only fire once per turn. And by using large numbers of missiles, it's even possible to present an AMS with more targets than it has the ability to engage (by exhausting ammunition or heat capacity).
But the actual missile attack is resolved with one to hit roll for the entire bay, so returning to our previous example of a bay of five white shark missiles, assuming the point defense is not able to engage every missile in the shot, what happens? Are any to-hit penalties accumulated by point defense applied to the entire bay as a whole, do the to hits for the affected missiles have to be resolved separately?