[Slick]

You have some (minimal) control over this. When setting up ship strategies, you can set the damage percent per ship (and planets, etc). The AI will make an attempt to direct weapons fire to accomplish this. The default is 80% damage to ships. With beam weapons, this is a little flakey, with missiles, you more often than not will exceed the percent damage and often destroy the target. This is partly because the AI doesn't take into account missiles that are in flight.

As an aside, this is why missile fleets are bad for capturing planets. They tend to glass them.

Of course, as stated, PDC is easier to use and cheaper to get to nerf missiles.