I'll just use my crystal ball and predict the future...
Seriously, though, I don't have a clue. I wouldn't be surprised if it just didn't work outright, or only worked in DS-mode with a firmware update. In fact, the latter's the most likely situation. Even if the 3DS gets hacked at any point in the DSTwo's update lifespan (most likely the next 18 months or so, judging by the average shelf life of Supercard products), the Supercard team most likely won't add 3DS support to the DSTwo. DSi mode support, maybe, but it's a big maybe.