Not 24 hours since its release, here's the Nintendo 3DS running the notorious R4 flash cart. It's not that much of a surprise - probably doesn't even qualify as a hack, as a 3DS is fully backward compatible with DS cartridges, essentially what this is.
But this does let you know that, yes, for those who
pirated ahem, "backed up regular DS cartridges they had legally and fully purchased," the device will work on a 3DS. 3DS games, which come on a cartridge that is 2 GB in size and shaped differently, remain, as far as we know, uncracked on day zero.
Nintendo has battled against the flash carts through the years, blaming sales drops on piracy associated with them and going to court to wipe out their business. They last tried to shut down the R4 and other flash cartridges with a firmware update back in December. R4 cracked that with an update of its own.