Then how would signing save data let us run Homebrew and stuff?
Look up the Twilight Hack, an exploit for the wii.
Sometimes you can modify the save data and when the game loads it, it does stuff it's not supposed to. The Twilight Hack had Epona's name (iirc) so long that the game crashed and allowed homebrew to be ran.
In the 3DS case, you can't just replace a save file, you need to sign it before the 3DS will load it.