I think the fear of being located isn't based on the fact that someone can decrypt an encrypted transmission, its simply because someone can trace that a particular location is transmitting some radio waves.
The transmission itself would need to be stealthy or separated (by distance and/or time) from the pilot. For example, the pilot might leave a transmitter to send a message "moving south, will hide on X hill" hours after the pilot leaves, or even toss a transmitter into a river. But most likely just very spread-spectrum/CDMA to make it indistinguishable from noise.