When you connect to the Internet, Nintendo can then see what systems have been playing pirated games and remotely disable them via firmware update.
The Enterking site posted this warning:
Dear customers who resell Nintendo 3DS:
Non-purchase able 3DS system: 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 a record of illegal or unapproved equipment.
To protect from leaking your personal and internet connection information we ask customer to format system.
Nintendo responded to the article with the following:
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.