The AES and CD Systems use +5v. But the Old-Style and Pro-Style joysticks are supposed to work with either +5 or Ground; so you should be good.
JHendrix's Guide:
"Now this is important because now I can plug Neo Geo home joysticks (the old style or the pro style) into my SuperGun and have it work just like my home built sticks would. As a note, you can NOT plug in Neo Geo CD pads into the SuperGun and have them work, more details on why later.
"Neo Geo joysticks will work with either Ground or +5V as they're common. The Neo CD joypads however do not work with Ground as a common, they actually require the +5V to operate."
Hope that helps,
-Kickin|wiNg