No, once you've done the qr code the first time on Cubic it creates a save file that when accessed will automatically load the homebrew channel - so you only need to do the qr code bit once.
lol... emulators... I don't think they really care about emulators on the 3ds - there are far more people running emulators on their android/ios devices; they're hindering eshop sales too, but Nintendos not doing anything about that.
I'm not saying that they won't at some point do something about Ninjhax, but you flat out stated that it WILL be patched in the next update and that's just speculation/scare-mongering.