Missile production costs
The cost of missiles. Like shipbuilding costs, missile production costs have come down, not increased, on a per-unit basis, even allowing for the introduction of new types. I'm not saying that a new type of missile is cheap when it's first introduced, because it isn't. You not only have the development costs, you have the need to make adjustments in your missile production, although what Manticore has been doing (by and large) is simply putting together a brand-new missile assembly line as the new birds come into production. That's really where the production bottlenecks which have been discussed, upon occasion, in the books come from. Once those production lines are up, they are largely 100 percent automated, and, once again, they're churning out their product in enormous numbers, which allows for huge economies of scale. I'm not saying these things are cheap, but an all up Manticoran MDM (I'm not talking about the Apollo control bird here; that's specifically exempted for reasons I'll touch on in a moment) probably actually costs the RMN less than the single-drive shipkillers (size for size) available to it at the time Honor went to Basilisk Station. When you're buying so damned many of them, the absolute cost for ammunition for the Fleet is far, far, far higher than it was at that time, but the cost per weapon (once the initial lead costs are absorbed) is far lower than people seem to be assuming.
The Apollo control missile, at the moment, is in an entirely different category, but that's because very few of its components and specialized technology represent mature technologies at this time. As production proceeds, however, the per-unit cost even of the control missile will drop steeply. It will probably never be as low as that of the attack missiles it controls, but that's because what it's stuffed with is basically more expensive than the attack missiles' laser heads.
Please note also that the difference between an EW missile and a shipkiller lies in the "warhead"/terminal bus fitted to it. That is, "warheads" are manufactured separately from the missiles and then mated, and most warships carry a substantial number of "spare" warheads which can be changed out with standard laser heads to meet current mission requirements.