Its funny because mods have some pretty cool large missile mounts, like the trebuchet launcher which is probably hella OP.
What are the best missile ships? For example I really like having a Conquest capital ship around because it has 2 large missile and 2 medium missile mounts which amounts to a pleasing amount of missile spam. It seems any small ships with medium universal mounts I stick missiles in there and try to get some good missile spam going.
Really I just like having tons of missiles fly around while I pew pew in a sunder or karkino
In vanilla, you are pretty much stuck with Vigilances. Which is fine, since medium missile mounts are probably all you want in vanilla. Some people might mention the Doom or Venture, but they are no where near cost effective and only even decent for about 5 seconds.
Mods, I recommend the Junk Pirates' Hammer or the Interstellar Imperium's Decurion at the frigate level. The Decurion is a little more survivable, but costs twice as much logistics and doesn't have the fast missile racks.
The Citadel Monolith is my favorite Capital level missile ship, with 3 large and 7 medium universal slots, and umpteen million small fixed point defense slots, you can load it with whichever missiles you want and it doubles as a great fleet support ship. It's not nearly as efficient, but it's a lot hardier than the frigates.
There aren't really any good destroyer/cruiser choices AFAIK. The cruisers are generally less efficient in terms of slots-per-deployment-cost than the monolith, so you might as well have the tougher and more all-around useful capital. There are very few destroyers with large slots even in the mods, and they can't compete with the frigate swarm's medium slot firepower. None of them that I know of would make a good missile ship.