The DSTWO works on the 3DS, and pretends to be a different game, ostensibly leaving no trace that a flash cart was used (unless Nintendo decides to punish everyone who owns a game that a flash card spoofs as, which they would not do).
However, you need to "flash" the card by putting it in a regular DS first (and downloading certain files onto it beforehand), so if you don't have one of those, it won't work on the 3ds to begin with, and will show up as a flash cart on your activity log.