According to Japanese retailer Enterking, a system update could render your 3DS unusable if you've used a DS flash card.
A Nintendo 3DS system update could potentially brick the system if the update detects traces of flash card use, which are often used for the purposes of playing pirated software. Japanese retailer Enterking has posted a warning on their website as follows:
"Dear Customers who resell Nintendo 3DS:
In case if you use equipment which is illegal or unapproved by Nintendo, or if you do customization which is unapproved by Nintendo, there is a possibility that Nintendo 3DS become non-bootable by system update."
The warning continues to state that because of this, Enterking is unable to buy a used 3DS if there is any trace of such usage. Users are to format their system before bringing them in to sell them, noting carefully that they will not be held responsible in the case that a user formats their system, brings it in to sell, and is declined, leaving the 3DS owner with a blank system.
Nintendo declined to comment when asked by Eurogamer about the potential countermeasures:
"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."