Just add 4 toxic injectors to your ship.
Takes out cruisers in one hit...
The current balance on missile weapons is a little broken. Mostly to do with point defence only targetting the first missile, irrespective of how many point defence guns you have.
However, too strong a PD will make missiles useless. Given that the average ship can send out a max of 4 missiles in a volley, and you can't easily synchronize the offence from more than one ship, saturating PD is, umm, difficult.