I find this topic perplexing and starting to get me a bit paranoid about my own personal odours! I have never had trouble with smelly footwear as far as I am aware. My cycle shoes are probably around 10yrs old and the closest they have been to having a clean is receiving a good hosing out after a muddy mountain bike ride then thrown on top of the boiler to dry when/if the heating comes on. If they get wet on my commute same thing, pull them straight off my feet and onto the boiler. I am sure I would notice if they did smell strongly of anything, I do occasionally notice I get a bit whiffy after a hard days physical work and we have a cat and I can tell if she has let me down and left a damp patch somewhere.
I wonder if the problem is more personal? I am not questioning anybody's hygiene but everybody is different and maybe the make-up of one persons sweat contains something that is causing the odours?
Sunlight is nature's disinfectant.
I'm not sure about this. Water has to be stored in dark containers to stop the formation of algae. When travelling, water cans should not be clear or uncoloured polythene as the water soon goes off/green.