Tracking
Not sure if all or any DME stations have recording facilities but it could be possible to ID an aircraft from the DME pulses. Each DME transmits an unique set of pulses specifics to the transceiver.
The pilots obviously knew what they were doing if it is eventually found out that it was stolen / hijacked. My guess anyway.
Probably used JepView on an iPad connected to a Bluetooth GPS to navigate.
If the guy was into flight sim etc, no doubt had Jeppersen on his iPad. Or any other multitude of standalone map apps.
No need for any Flight management transmissions to give their position away.