Nintendo is specifically trying to make sure that piracy is impossible on the 3DS. This means no execution of any code that Nintendo doesn't approve. The side effect is that we have no Action Replay, and it's hard to try to inject code into a save file to run homebrew from that. Ever heard of Sudokuhax? It exploited the save file of a DSiWare title to enable homebrew. If it wasn't patched (disabling transfer of save data for DSiWare titles for everyone), it very well could have led to piracy through the SD card slot. Now that I'm thinking about it, the CycloDSi actually managed to run pirated DSi titles using a save exploit on a DSi game.
Long story short, hackers either need to find a good exploit* or somehow convince Nintendo to sign a cheating device that could ruin online play in the wrong hands. I don't see Nintendo doing that.
*There's one found by the Gateway team, but only works on the 4.5 3DS firmware and was fixed before it was released. 3DS homebrew is still not out, but there are screenshots of unsigned code running on the 3DS using the Gateway exploit.