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.
You encrypt it because encryption is cheap and gives you confidence that the message content won't be intercepted.
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.
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.