Antimatter blaster requires the ability to close in range, so either phase ships or very fast ships with survivability. I've had quite a bit of fun with Wolf, Scarab and Aurora with AM blasters, though you have to accept the high risk of losing the ship. Phase ships of course trounces all in using AM blaster. I also suppose AM blaster with the Monitor is possible, though I've never tried doing so. AI controlled ships rarely uses such ships to its full potential, though once I had a missileless AM blaster AI Aurora run straight up head to head to a fresh Dominator and immediately destroy it without any damage whatsoever, though I've never been able to replicate that since. But ultimately it's not the ammo count that makes AM blaster a niche weapon, it would be niche even with no ammo restrictions at all.
As for the Doom, it does seem strong in many circumstances. If the purpose of deployment cost (which it may or may not be) is to balance out the widely differing designs of ships, then a simple fix would simply be to increase the deployment cost to something more reasonable. Like 40 for example. Alternatively increase the flux increase of mines, or decrease the radius, but deployment points is the simplest, though may not solve the problem of being widly effective in some situations.
As to whether missiles should have limited ammo or not, missiles don't cost any flux to fire, so things like Annihilator Rocket Pod would be obscene, especially when the best tactic vs it is to either take out the ship holding it immediately, or just wait till it runs out of ammo, so missiles like that should have a flux cost to fire, taking away 2 unique characteristic of missile types. I guess i don't like the design of Annihliator weapon pods. Anyways, personally I don't like any of the large missile mounts; I usually find that I leave them empty unless there is a lack of weapons otherwise.