The idea of the armored missile is that it is a deep-strike weapon, which lets you attack any enemy target (that you can "get eyes on" through other means) with impunity, but with then incurring an AI Progress cost. The mechanic, I think, is sound, though the amount of damage it deals maybe should be quadrupled or something. It's still not something that would ever be that commonly used, and that's by design, but it's meant to be one of those "weapons of last resort" sort of things.