I would guess worse, but in different ways. Your foot can shift in the sand left/right when landing, causing havoc on other joints (knee, hip) when you apply pressure and they're getting unexpected horizontal motion.
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.