I remember a while ago when digital amps were relatively new, there was some "controversy" using small digital amps to drive K1000's, for some of the same reasons, mostly the ultrasonic noise. I used a digital amp for a while with my K1000's, until the amp broke. Never bothered me.
I currently use a tube amp. I think it sounds better, but is much more expensive than the digital amp I had.
I'm not a doctor, but it seems that if it was really bad for you, there would be some symtoms, like headaches, before you had permanent damage.