Ponies had to walk through the metal-detector-looking thingy to have the disabling spell applied– I don’t think they’d make the movers of sun and moon walk through a metal detector…
I don’t think the Princesses are good flyers. We hardly see them do so for any length of time, and we know Cadance isn’t in shape—not even compared to Twilight ‘I-had-my-wings-for-less-than-a-year’ Sparkle.