Heavy missiles don't work that well on big ships because if something travels behind the missile it loses track of its target (I'm not sure if this applies to all missiles).
If you're looking for megadeathweapons, maybe a battleship forward gun would work better?
What I think would be a cool addition, in the vein of the vertical torps and cap torps, are close-range, slow, broadside-style cap torps a la the capital ship fights in Starlancer. Sort of close and dirty capship knife fights. Admittedly, I just have a fondness for Starlancer, but hey.:P
"Things will not calm down, Daniel Jackson. They will, in fact, calm up."