According to GoNintendo, Japanese retailer Enterking has posted a warning on its website suggesting that Nintendo will brick 3DS consoles suspected of monkey business. Loosely translated, the site says that anyone who runs software or makes modifications unapproved by Nintendo might receive a firmware update that renders the 3DS unbootable. If true, it's safe to assume Nintendo is largely aiming at folks who use R4 flashcarts to play pirated games, which has been outlawed in Japan and the UK.
Nintendo issued an ambiguous statement to Eurogamer, but the company didn't confirm whether the 3DS has some form of killswitch. "We do not discuss product security details (for obvious reasons), nor can we discuss the details of countermeasures available in the Nintendo 3DS system," a spokesperson said. "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."