Flash cards don't work that way and Nintendo can't (and doesn't) legally brick things on purpose.
There's nothing current piracy devices do that touches anything in the system software; you can't access the kernel at all from SLOT-1 on a DS or DSi, and it's probably the same on the 3DS.
If that's not the case, it won't be long before someone makes custom firmware or something like the Homebrew Channel, at which point thousands of users will void their warranty by installing the unauthorized software, void their bowels when their systems stop working come update time, and whine like three-year-olds on the Internet when Nintendo doesn't replace their bricked 3DSes.
You know, exactly like what happened with the Wii.