Actually, I use cruiser missile turrets exclusively on my gunboats. Sure, they eat almost all my power in one salvo, but the resulting explosion is well worth it
Thing is, missiles arent worth anything if you cant target your enemy. As it is, most of my missiles go astray, so unless my target is almost right in front of me and heading either away or preferably towards me, they dont hit anything. And with the changes to gunboat manoeuvrability, Ive found that the best tactic is to simply kill my engines, switch to turret mode and then wait for one of my enemies to approach me head on. And even then the chance of hitting him seems very slim.
Thing is, when your best tactic is to sit still in the middle of a large group of Titans, then things get interesting very quickly