The card itself is not banned in normal play; it is restricted on PTCGO due to a game-breaking bug involving Klefki STS (if you Ninja Boy a Pokemon with Klefki attached to it, Klefki will not only remain attached to the Pokemon you shuffle in, but it will stay attached for the rest of the game).
It should be fixed with the next PTCGO update, which should be coming soon. Not sure on the exact date. I should note that Ninja Boy is only banned from matchmade opponents. You can use it with no restrictions in friend matches.