I've always squatted deep, because of flexibility that happened to be there already (no idea how or why, but I'm not complaining!) and yet, there's been a couple of guys at the gym who've insisted on commenting on the way I do squats - negatively or "oddly", that is.
The first was a guy older than me, who claimed (and continues to claim) that squatting below parallel AT ALL will kill your knees, regardless. And guess what? That's right: his knees are shot, apparently. But... I doubt he killed them by squatting low. Oh, and he doesn't do any kind of squats. Ever.
The other was a guy younger than me, fairly strong in general (though more in the upper body area, by far
), and who thought it was just bizarre, and also "brave" or something along those lines (i.e., I'm totally insane), that I squat "so low". And guess what? That's right: he does some half squats, maybe once a week - if that! - and calls it a day.
The only other people I see doing actual full barbell back squats* (high or low bar; whichever), funnily enough, never seem to have any issues with their knees. And yeah, I don't either, and never have.
* The ones that persevere with lifting and learning about it, and therefore don't have horrendous form, I mean.