I mentioned this in another thread, but Nintendo got all the information they needed from the initial announcement. A game save exploit and a hacked crash screen. They went back and looked at any permissions the 3DS has while playing games and found where a game running would be able to get kernel access. Nintendo likely patched the hole by changing permissions for 3DS games or the crash screen, which could have been running in kernel mode(something like leaving the keys in the engine of a car.) The architecture is closer to a computer than the DS line of systems so they have the capability to fix these things. They can still use the save game hack to run code, but they no longer have kernel access.