Cruising altitude is ~40k feet or 12 km and the range of the weapon is 2km. The system only works because of all the exposed wiring on quadcopters; everything in a plane is enclosed in a highly conductive aluminum shell and is very well protected. The windows are large enough to let in microwaves, but not very well. Some antennas might be in danger but in general planes are built to survive lighting. It would be a real freak accident for something to break.
I'd be more concerned about small planes or other drones. But if a little shielding fixes it, then this will quickly be obsolete as it's trivial to dd shielding if you're a malicious actor.
Lasers and masers are not inherently collimated or straight lines. The only thing specific to lasers/masers is that all the light is the same wavelength. Beam, parabolic and phased antennas are all very capable of making much tighter beams than your average laser.
In fact at the limits of performance lasers (and particularly masers) are quite bad at generating straight beams, because they are quite small sources of light and divergence is inversely proportional to the width of the emitter. It is a misconception that they are low-etendue.
Lasers are coherent emitters, which means that they behave like a perfect point source and the beam forming is limited only by diffraction. The collimation is limited only by the lens diameter and quality.
I assumed they would be masers or at least something with high directional gain. Otherwise your zapping a bunch of other stuff. Someone else said it's only a 2km range.
And also - what about the payload that drone was delivering, aimed at the target and doing 150kmh or more when your microwaves zapped it and killed off all the electronics. It'll only take it 2 unpowered/unguided seconds to cover that last 100m, so it'll have dropped 20m on a ballistic trajectory. It won't have hit your tank right in the crew hatch, but it's still delivered its explosive way too close for comfort. Perhaps not a problem if the target is an armored vehicle, but it'll probably still set your ammunition store or fuel dump on fire.