No but autohotkey can't block keys in any version of windows newer than XP.
So if using Vista or newer, those keys would still be registering in addition to the ones you changed them to.
When I had an x-arcade, I set up an alternative mapping to avoid things like this.
If you have an older one, you have to press the button on the back twice to load the alternative settings which sucks, but at least you can change the keys.
The new ones don't require you to do this.
This is why I never use the first four default MAME keys.
It just leads to problems with other games and emulators.