I run barefoot all the time on the beach, at the water line when the tide is lower so it's nice and flat and you can see surface well.

I have no problems with my shins and knees since I'm running mostly mid to slightly forefoot strikes. The forefoot absorbs the shock rather than pounding the knee and hip with a direct impact. When I run with shoes on pavement, I get some knee and hip issues, especially if I don't pay attention to my foot strikes with respect to changing pavement.