The best shoulder protection probably involves some sort of football or hockey shoulder pads. Unfortunately, they are not very practical to wear.
I've tried high-end hockey pads (Bauer Supreme 5000), and they are just too big and bulky. Plus, they'd be extremely hot in the summer, and fabric covers the plastic pads, which would get torn up pretty easily in the woods. I could not fit the pads under my normally sized riding jersey.
I did buy a set of cheap hockey pads, and I am going to try to remove the plastic shoulder pads and somehow rig them up to my Thor Aftershock chest protector. Definitely room for improvement on the shoulder area of chest protectors.
In the end, we can only take reasonable and prudent precautions regarding protective gear. The shoulder/collarbone areas are still really easy to injure. Even with over-the-top protection like football pads, it only takes a small amount of force at the right spot and right angle to break a collarbone or separate a shoulder.
I've broken my collarbone a couple times, and that really motivates you to be a better rider!