What is the fundamental physics behind L/D decreasing as AoA increases beyond the optimal point?
The fundamental reason is that at high enough AoA, the lift becomes zero -- certainly no later than an AoA of 90°! At that point L/D is zero (there'll be lots of drag). So somewhere between 0° and 90° there will be an AoA with the highest L/D, and that is by definition the optimum AoA. Slightly beyond that angle there's nothing for the L/D to do except decrease, because if it didn't, the angle we're beyond wouldn't be the optimum.

Now if you were asking why that particular angle is optimal for a given airfoil, we would have to go into aerodynamics and boundary layers and whatnot. It's not merely about what happens to the molecules that (try to) hit the underside of the wing, but at least as much about how well the molecules above the wing can be convinced not to hit it.

Note that above the optimal AoA, until the critical (stall) angle, the lift generated still increases with increasing AoA -- it's just that in this range drag increases faster than the lift does.