I mean, that's true until it isn't. Autonomous drones (otherwise known as weird looking missiles?) being used to attack a base with a fancy microwave air-defence system isn't really science fiction anymore.
I suppose cameras might be hard to shield too?
Guidance via camera has been a thing for a long time: https://en.wikipedia.org/wiki/TERCOM#DSMAC,_Digital_Scene_Ma... I don't know if it's available open source (or commercially), but I don't imagine it would take me (or any other reasonably skilled programmer) long to develop it these days. Satellite imagery is freely available from google maps if you have nothing better.
Near(ish) peer adversaries (the kind that can afford drone swarms) are definitely capable of the guidance part.
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?