They probably nuked it because of the (in?)famous Animal Crossing: New Leaf cloning
glitch where you could dupe items by turning off Wi-Fi at a specific rotation of the throbber.
Doubt it. It's more likely because it goes against the "always connected n' stuff" approach of the 3DS. Nintendo are slowly pushing the idea of "keep your console on, and get demos, news, updates, marketing material, etc", and turning off the Wifi so easily goes against that approach. Yes, you can delete your connection settings, but for the average clueless user, it's a hassle with no apparent benefits.
The spotpass of the 3DS was the first implementation of this approach. This proved successful, so the Wii U was the next step. Now we have marketing information exploding in your face right at the home screen, and I had to turn off the automatic software download because Nintendo uploaded a 1GB demo of Wii Sports Club without asking me if I'm even interested.
Also, it'd be extremely easy to implement failsafes within games to prevent duping. If any stage of the transfer is not complete, undo the transfer. It's amazing that this kind of glitch still exists frankly.