The effect of an EMP on a hardened i.e. Faraday cage-shielded target is quite limited. Even modern automobiles are only momentarily disrupted, if at all, by significant pulses produced in a controlled test setting. As I understand it, common measures taken to protect vehicle electronics against electro-static discharge (ESD) also provide some level of protection against EMP attack. Your mileage may vary with commercial off-the-shelf drones, of course, but it’s not an expensive or difficult technology to retrofit.
My understanding derives chiefly from a U.S. government-commissioned study on the effects of an EMP weapon or natural disaster on things like cars, trucks, airplanes and computers. The results were made public, and are overall fairly reassuring:
Reassuring until you realize that 0.1% of components of a complex system failing is likely to bring the overall system down.
In this case: Individual controllers needed to control a power plant or factory, as well as "individual cars on a highway" (once enough break down, the highway is blocked).
My understanding derives chiefly from a U.S. government-commissioned study on the effects of an EMP weapon or natural disaster on things like cars, trucks, airplanes and computers. The results were made public, and are overall fairly reassuring:
http://www.empcommission.org/reports.php