[nonethewiser]

How much do the direction/location of the antenna and incoming pulse matter?

The antenna could point up and communicate with satellites. Meanwhile the pulse will be coming from underneath. Maybe it could be diffused off to the side?

[giantrobot]

A high power microwave beam will pass right through plastics and composites. Unless you add a lot of shielding, that microwave pulse can and will induct a charge in wires and electrical components. Shielding is heavy and makes a drone easier to detect.