EMPs are not that narrowly targeted.
Law enforcement has for years used EMP RCC's (Radio Controlled Cars) that "detonate" near or under the car being chased to blow out the car's electronics. Not used very often because of the expense of a one-shot RCC because it too "blows up" electronically.
The authors would like us to believe there is some intent or capacity for Feds to EMP large areas of the country.
Whatever that U-2 may have done to affect FAA systems, I doubt it would be categorized as an EMP.