The 3DS was apparently already cracked within 24 hours of release, and it's now supposedly running piracy devices. Isn't Nintendo going to do anything? You betcha.
Back in July 2010, THQ's Ian Curran said, "What excites me even more [than 3DS games] is that there's technology built in that device to really combat piracy...I actually asked Nintendo to explain the technology and they said it's very difficult to do so because it's so sophisticated."
Fast-forward to 2011. Japanese game retailer Enterking issued a notice that it would not be buying back any 3DS units that were used with a R4-type devices - specifically "illegal or unauthorized devices". The notice states that there seems to be a record of such use left on the system. This would be in line with the rumors that the 3DS keeps a log of flash cart use, which then can be checked.
The Nintendo terms of agreement clearly state that it is possible that the 3DS might not be able to boot up after firmware updates if unapproved or illegal devices are used in the 3DS. You have been warned!