This isn't really for drones. It's for frying ground-based electronics like cell phones. Drones are the smoke screen to hide that fact.
As for drones, motors and batteries are quite hardy against quick microwave pulses. A bit of aluminum foil makes a good, light Faraday cage. Optocouplers can isolate radio and GPS modules from the actual motor control systems.
I would expect you can fry an RC drone, but an autonomous one operating inertially or capable of switching so when radio/GPS goes away is probably pretty easy to shield.
In addition, this kind of system is always going to have a range vs width tradeoff. Can the drones get inside this thing's range where they can still be effective even if they are "ballistic"?
Dumb old bombs are really effective if you just give them a little bit of GPS to improve their accuracy. You don't have to get very close for the GPS adjustment to be devastatingly effective.
Or imagine a smaller system integrated on a humvee that can destroy electronics in anything along the path a few dozen meters in front and in a smaller side/side area. That'd end the IED threat from anything other than a purely mechanical IED (not sure if many of those are around anymore, as everything assumes electronics will work nowadays).
This is why IEDs are so effective in asymmetric warfare. They are cheap and anyone can get parts =(
The first time I saw the results of an IED blast was a day after I arrived in Iraq. I had to shake a tree in order to retrieve the trousers of the guy who blew himself up planting the thing. That happened a lot. Making IEDs isn't very hard, but making a lot of them without eventually blowing yourself up is.
Now a much better thing to do instead of making IED drones would be to melt sand or rock into appropriately formed projectiles so that one has an autonomous artillery piece that does not require reloading.
There are much better explosives to use than hydrogen. One could use the haber process to make ammonia and use some biological carbon sources to make pretty much any explosive worth using.
Landmines are probably cheaper though.
While I agree with the idea that there will be more fun ahead with ground-based drones, wouldn't an air-dominance doctrine still hold in drone-drone warfare as it exists today in conventional wars?
I imagine both ground and air drone warfare evolving at similarly terrifying rates over our lifetimes.
The US relies on air power tho if you look at BDA imagery released not a small percentage of the so called drone strikes are more likely than not to have been conducted by mannned strike fighters as drones can't carry things that would leave that big of a crater.
I don't mean that air-based drones will be useless, I just think they're going to see more constrained missions than we might currently be imagining. And I do mean just the common conception of drones... things arguably properly described as "autonomous planes" will continue to be important and will probably continue to grow both in importance and in physical size.