There are specialised ship classes (as shown on previous page with Rostov gunship variants) that take a role of missile/energy or standard ship. Sticking a single missile (that costs almost nothing in creds and points and does 600 points of kinetic damage) to a frigate with lots of explosive guns will greatly increase its performance. You can always go kinetic/explosive combination of weapons (that`s how the majority of ships in campaign are set up) to balance things or go purely energy (and be forced to deal with flux), but it is funnier to go other ways really.
And there is nothing more funny than disabling a forward oriented destroyer with lots of fixed hardpoints with a single hit of EMP heat seeker missile and consequent bombardment of it with explosive guns
P.S.
small missile mounts most of the time have a 1 shot missile launcher, exceptions are anti-fighter missiles that come with 2-shot launchers, rocket racks and expensive torpedo tubes.
medium mounts have a 3 shot launcher for standard missiles, single shot launcher for large missiles (MIRV/cruise), 3-4 tubes for torpedoes and batteries of 10-15 rockets/anti-fighter missiles.
large mounts carry huge launchers with up to 20 standard missiles, 3-5 cruise/mirw and batteries of torpedo tubes.
I`ve eliminated small sized multiple missile launchers moving them one tier above. Those just don`t fit well with all the fighter concept Ironclad mod has. (fighters usually carrying 1 standard missile and/or 2-shot anti-fighter missiles).