I had something happen once a couple of years ago with ours. It started making strange sounds, not all the time, but often. It seemed kind of like a brake grinding sound sometimes, sometimes more of a brake squeal sound.
This had started happening abruptly, not like a gradual thing like the pads wearing down into the rotors. Like you, we don't really use the brakes much at all either, with the HST just not needed - other than we use the e-brake regularly. I thought perhaps the e-brake wasn't releasing all the way or something, but everything seemed to be working ok from what I could see.
Guess I'm making a short story long. It turned out, after a bunch of searching, that I discovered a small stone had somehow managed to drop into the space between the rotor and that plate-guard thing that wraps around the lower part of the rotor. I could just barely see it with a flashlight down there. I didn't want to start taking stuff apart, and was able to eventually fish it up and out.
Don't know how it managed to flip in there, and haven't ever had it happen since. Anyway, something you might want to look for...