Nintendo, like most companies, takes a palpable stance against piracy. We recommend that those fortunate enough to own a 3DS stay away from the flash cards altogether, just in case."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.
Update: Flash cards aren't illegal to use per se -- homebrew, anyone? -- although certain countries have banned them from import and sale, and their widespread use for illegal activity makes them a dubious proposition quite often.