Built an HAC spam ship the same size as the Canon GATC, and its about 80% loss for the Canon.. the arc that the missiles fire in seriously screws over my side armour, but the fact that all of your launchers are attached to a single sprite means when the AI is trying to get through to the core it invariably knocks it out. If you spread them out, or put them closer to the back I think that it would probably skew the other way by quite a bit.. missiles are so damaging when they can hit less armoured areas around the sides.
Looking at the way the missiles move though, I think the heavy missiles may track a little too well, as when both ships are nose to nose they can still hit the forward-most parts of the other ship easily.
EDIT: thinking on it though, they will generally only hit the front of the opposing ship when firing at range, so their lower DPS:power & mass ratios will kick in and make them less effective. Wouldn't really have thought they'd be better at short range.
(trying to fit 45 Heavy Autocannons onto a single ship was a pain