Is going clipless shagging my knees?

I know a lot of cyclists that have broken collarbones.
It's a bit of a stretch blaming knee pain on your pedal system when cyclist's knees get caned through normal use and any number of factors might be at work here.

Not that much of a stretch. A young person, still growing uses a pedal locking system with no lateral float to anchor their feet/knees in a static position whilst exerting all sorts of forces on these areas. Over a period of years,damage may occur. I dont know any cyclists with broken collarbones.