I wonder how effective an EMP would be at "sterilising" a vehicle of such trackers. Especially if the vehicle in question has no electronics and uses a mechanically-injected diesel engine.
Diesel's going back 20+ years still have ECUs as well, not to mention the rest of the vehicle's electronics could be at risk. So it would have to be a properly old or unique vehicle.
That said, whilst it is a known threat vector, I have no data on how often its actually exploited. It might be a lot of work for nothing.