If your shoes are already getting stinky, you can kill the bacterial growth in them and get a fresh start. Sounds yucky, but you can put them in a ZipLoc bag and put them in the freezer for a couple of days. Take them out, spray them with antibacterial spray (Lysol, foot spray, whatever) and put them out in the sun. UV rays kill off lots of bad stuff, so open the tongue of the shoes if possible and let the light shine in.
Maintain with regular spray and occasional freeze treatments.
Advice from your local OCD climber!