Yeah, they are costly to mount, but Scy ships have a lot of OP for few weapon mounts: A 16 ordinance points weapon is for them almost the same thing as a 12 points weapon for a vanilla ship. They also often have a longer range than the basic Scy weapons. As for ammunition: if you put 4 of these emp missiles on a single Orthrus with missile rack (can get done with the default points, no skill involved) you get 40 missiles, or 20 salvos. Enough to cripple a tight group of ships during like 20 seconds. I'd say this is really powerful enough. I might even nerf them a bit.
Per design choice, most of Scy ships will be equipped with the "standard" weapons (auto nailers, KACC, HEMOR, rockets launchers, and probably Energy blaster) Those have a fair price, a fair amount of rounds, and cost fewer OP to mount. Then some of them will sport the much more fancy recent weapons. Those will be elite ships, meant to give an edge and keep players on their toes. I can tell you that in my playtests, those weapons gives a huge advantage if only for a short time: slashing beams can hit all engines at once, in a couple of shoots you are almost assured to flameout your target. The area scorcher is of no use against armored target, but it eat hull for breakfast, and kill fighters as they leave their hangar. The ricochet gun can get you rid of those annoying shielded frigates... So yes they come at a price and probably won't win the war for you with so few ammo, but they are certainly not to underestimate. Besides, they look great and are terribly fun to use!
That being said, there is always room for balance improvement and I'll keep an eye on it, but in this case I suspect I'd have to nerf them before increasing their ammo.