1) Coat the walls and ceilings with steel backed teflon. If the steel isn't thick enough, they can still use their claws. Make sure it's at least a 1/4 inch thick.
2) Install random rotating magnets. This makes it difficult to throw shurikens accurately.
3) Set up a DVD of old "Kung Fu" reruns in infinite reply. Warning: This may cause Seppuku incidents, which are really messy. Take my word on it. Spread plastic in front of the TV.
Avoid using pirates. I know it's tempting, but they're worse than ninjas (really loud and smelly and treasure chests are hard to find).
Bill: Sorry, spent all day Saturday Ninja Proofing.