Ha, not likely. Unless nintendo finds a way to patch these hacks soon (I hope they do), piracy will be rife again, and online games will become unplayable. So help me, if someone invents hacks for KI: Uprising, I will be incredibly pissed.
They do, it's called firmware updates. With these kinds of hacks, there will always have to be a fixable vulnerability that they're exploiting or something that's detectable and blockable. This will probably be an endless battle from now until the 3DS finally dies, but it's a battle that Nintendo can fight.