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:

http://www.empcommission.org/reports.php

Outside of scifi plot devices I don't see how that would be feasible.

EMP is not a practical mitigation. That's something that works in movies, not real life. Generating an EMP powerful enough to damage electronics requires a large explosion to pump the coils. And even then the range is very short.