I honestly believe they have done it to combat piracy.
All Nintendo handhelds were region free before, but then came the devastating piracy on the DS. The DS Piracy was likely the worst of any device in history. Even in the worst days of the PS1, PS2, Amiga etc, you didn't have mothers buying $15 piracy devices for their young children that instantly allowed theft of 200 games on a single $10 SD card. No risks of bricking, no firmware updates, no hardware mods, no complicated copy procedures, just a $15 cart, drag and drop.
They have definitely added it to the 3DS because they feel that any flashcarts would still be locked to a region unless both locks are broken. As most piracy is centered in asia, the flash carts would be locked to asian 3DSes. And there the motivation ends for asian-centred manufacturers. So even with a crack, piracy remains quarantined to one region.
And this is playing out. All 3DS cracks and prototype flash carts so far have not been able to run outside of the hardware's region.
Don't blame Nintendo. Blame every single person you ever saw pirating DS games. Admitting to piracy seems to get you banned here, as does accusing others, but I have little doubt a huge number of people in this very thread pirated DS games. They caused this.