The Hammerhead in general has some pretty terrible flux capacity. You need to come in and out of engagement range a lot to vent. I'd say if you're going to run AM blasters, put a little into capacitors, and drop your shields sometimes. Not all the time, but sometimes-- the Hammerhead is pretty durable. That way, you can use all your flux to fire your weapons. Two rounds from AM blasters will put most destroyers into a state of real high flux, and after a few assault cannon rounds, they'll either be venting or overloaded and you can let your harpoons do the rest.
I flew the Hammerhead as my flagship all the way up until I caught myself an Odyssey, and that set up seems to work for me. If you do want a destroyer that can dish it out and take it, try one of the slower, tougher ones.