If you let the AI manage targets then they tend to not focus fire and will pick targets based on what they do the most damage to.
This has not been my experience when I've been playing, and I just jumped into a system where the other player had 14 ships and me with 12 light frigates, left to do their own thing, they focused fire on one enemy ship at a time, target after target.
Pretty sure that the shield mitigation applies to missiles that phase past the shield and hit the hull.
I ran some tests on this (which is hard in this game because you can't attack your own units for some reason), and found that the phase missiles ignore mitigation completely when they phase.
I didn't even take into account the fact that with 85% mitigation, the hull missiles would kill the hull while they still had shields left, so actually, on average, against a level 10 radiance battleship with 85% mitigation, the phase missiles as they are now would kill the ship 11 times as fast as the same ship without the phase missiles upgrade. That is not an exaggeration, that is right around the real number.