I'm not sure why I was thinking of this, but I did and I couldn't think of an equivalent physical model to relate microwaved liquid Mercury to.
Polar substances are heated by dielectric heating, the poles wiggle with the wave of the microwave and that translates to heat energy.
Metals spark in a microwave if the sea of electrons that slosh about find a differently charged part of the sea to jump to. Mainly between pointy part of the metal.
This is my '10 years post MPhys' recollection of relevant physics.
But the sea of electrons in mercury is also physically liquid, not just metaphorically.
I've seen videos of people attempting this, but there's no clear outcome besides "bang".
The question on the subreddit /r/AskScience wasn't super clear, besides stressing not to do it.
As for what'll happen in mercury...its extremely difficult to find a microwave absorption spectrum for elemental mercury. My suspicion, since mercury is center symmetric and non-polar, is that there won't be much dielectric heating since atoms can't sustain a rotational moment. You may get conductive heating though -- its quite probable that (like other metals) the microwaves will be of sufficient frequency to eject electrons from the mercury and start the conduction of electricity. This will also heat the mercury. So, the answer to your question is that it will probably heat the mercury, but not for the same reason that it heats food.
Does the eventually charging and conduction of electorns do anything structurally to the mercury? I'm somehow envisioning something akin to ferrofluids but for vastly different reasons... Localized electric fields?
This video on making mercury part of a circuit is wholly unremarkable, so doesn't reveal anything about what's happening at the atomic level.
So what does happen, on the atomic level, to microwaves mercury?