With no evidence, you're taking it as a given that shoes are protective of joints. Shoes are protective of skin. That's what they were created for. They stop you from cutting your foot on sharp stones.

There is mounting evidence that typical running shoes are bad for joints, because they encourage heel striking. Evolution is indeed limited, but it did a pretty good job of producing a structure that absorbs the impact from running. Modern running shoes short-circuit that structure by making it possible to heel strike, putting that impact through the knees and ankles instead of letting muscle and connective tissue absorb it. The think heels of typical running shoes make heel striking almost a necessity, because it's so awkward to forefoot strike while wearing them.