[gordner]

You can de-activate the transponders for sure. The point of the ELT is only valid if they did indeed crash, if hijacked and instructed to kill outgoing transmissions the aircraft could be turned fully black by the crew. Not as easy these days as it was, but doable.
And if it was an over-ocean at altitude take over then cell phones would be a moot point, one would expect they could remove all cell's from passenger before re-entering a service area, or they could employ a simple cell jammer.