I'm not clear what you mean by "work with Hyperspin". It sounds like you are using Hyperspin to run AHK scripts, but you actually want the hotkeys to be in effect when running an emulator launched from Hyperspin, right? More recent versions of MAME don't work with AHK, at least the pre-compiled versions don't. Possibly other emulators don't work with AHK either. If your AHK inside of HS is valid, then the problem is probably the individual emulators' compatability with AHK. I suggest running your AHK scripts and emulators without HS to investigate.
The last I checked, MAME can be compiled in such a way that AHK will work with it. There isn't a direct "work with AHK" flag, but googling MAME and AHK should point you in the right direction.