The Secret Key will come. The Official Nintendo Magazine states that it'll be given out via WiFi, and I doubt they would have said that if they weren't planning to give it out.
*points at the super-awesome-Rotom-part which also proves that Heat Forme Rotom IS AN OVEN, NOT A TOASTER*
The official Nintendo Magazine is Nintendo Power. That name is a lie. And besides, it's not even out yet. We wont know for sure until it is out, even though it's so highly unlikely they wont do it over Wi-Fi.