Shock absorption? That old line again?
Although I don't run barefoot for various environmental reasons - 'shock absorption' is actually something that footwear companies trawl out to sell trainers. The issue is not with the impact of the foot on the ground but with the technique that we use to run. Watch a man run barefoot and he uses a totally different impact point and ankle movement to running with training shoes on. Barefoot runners run on the balls of their feet and allow the knee to flex to its full capability. Most runners wearing trainers run on their heels more than is healthy. After runners have developed a technique to prevent running on their heels - even with shock absorbing footwear - the rate of injury drastically decreases. If nobody wore shoes then the 'natural' running gait that is used by the majority of people would change drastically to one that is more natural and prevents injury.
Of course, I generalise but actually if 'shock absorption' is your main justification for having to wear shoes then I'd hate to see your running gait. Pedals are at the very most medium-impact and more like low-impact. There shouldn't be any 'shock' issues with the ankles or knees.
I wear shoes because the stiffness of the sole allows me to control the pedal movement better but it doesn't make a huge difference either way and - as I said earlier - I'm happy playing without shoes on and can wear a wide variety of shoes and still play comfortably.
EDIT: Here's a partial source. I watched the documentary (probably not available in the US) months ago and it was fascinating.