The AI is pretty terrible at countering anything you do. You can probably do the same with beam tech etc. and win too, it's not a missile thing. If the AI beelined point defense, your fleet would be wrecked pretty fast. 

They shoot faster. Weapon damage isn't exactly balanced at the moment.

Missiles and Lazers are the clear winners, with missiles being a little bit better than lazers unless you abuse reloading then missiles are game breaking strong.

But overall it's sort of an apples and oranges comparison. They shoot at different ranges and are intended to be slower(missles than lazers). So the damage per second is supposed to be somewhat close.

I wish they'd actually show DPS,, especially for carriers.  Would help me decide what to build