According to a roughly translated statement from Japanese retailer Enterking the 3DS may be capable of monitoring when flashcards are used to play pirated material on them, as well as potentially locking systems which are caught doing so:
“Dear customers who resell Nintendo 3DS… If you use equipment which is illegal or unapproved by Nintendo or if you do customisation which is unapproved by Nintendo, there is a possibility that Nintendo 3DS becomes non-bootable by system update. Because of terms of agreement above, Enterking refuses to buy 3DS system with record of illegal or unapproved equipment.”
Nintendo issued a statement to Eurogamer regarding the post:
“We do not discuss product security details (for obvious reasons), nor can we discuss the details of countermeasures available in the Nintendo 3DS system. Nintendo 3DS has the most up-to-date technology. The security has been designed to protect both the creative works in the software and to protect the Nintendo 3DS hardware system itself.”
Thanks to CVG for the info.