I know there's no flashcart capable to run 3DS roms nowadays but... Could DSTwo do it in a future with a software update? Or it's likely to appear DSThree for example?
For those who care about the fix, before playing the game, use Pimp My Wii 2.28 and it will install all you need to the latest revision.
All games will work.
first of all, be sure you choose the correct partition. If it gets this error, use Disc Utility from Mac and erase any partition in the HDD you want to use.
Then try it again with QWBFS 1.2 I posted before.