Considering the 3DS hasn't been released yet, we don't know much about what sort of methods could be used for homebrew or piracy. At this point, it isn't a matter of "when a flashcart is made", but rather "if a flashcart is made". After all, the 3DS could never end up being exploited, or it could end up being exploited in a way other than flashcarts, such as cracked apps/firmware.
So, given the circumstances, it's up in the air as to what will happen in the future when it comes to the hackability of the 3DS, let alone if it's backwards compatible with the regular DS line. We'll just have to wait and see.