Seems to me the weak point of a hypersonic missile would be its targeting system, which, given that it is aimed at moving objects, would have to be external, likely satellite (or balloon, lol). Take that out, the missile just flies really fast for a while.
Negative. Optical pattern recognition is a thing, especially with modern AI - you could give it a general area prior to launch, or you could use a ground link to update. The missile doesn’t *have* to radiate and give itself away.