I think it is pretty hard to disrupt a drone that was designed to withstand EMP. It doesn't take a very heavy conducting shield to protect integrated circuits. And the penetration depth means it is exponential decay inside the shielding so you can't overcome it by simply using "more juice" unless you can create exponentially more juice. Jamming communication might be more effective. But autonomous systems are not so dependent on communication. And there are counter-measures to most common jamming methods. In short, the main vulnerability of drone air forces seems to be cost to engineer and build robust survivable drones. And I fear that vulnerability is not going to be enough to keep them from becoming very common.