Hey everyone, just a quick update for anyone interested.
KH3D is Circle Pad Pro compatible, however if you start a game without it connected it doesn't appear to register in game later on. If you start a new game with it connected it works pretty well though the camera controls on the right circle pad are reversed and I haven't figured out how to change that yet.
Circle Pad Pro is also not locked to a region so the NA works on JAP 3DS and visa versa.