Dr. Del, I think the increase in RI seen around breeding has a lot to do with stress, as well as the other factors you mentioned.
RI's in mammals and birds are often spread by aerosol -- that is viral particles or bacteria are spread into the air with sneezing and coughing. As was mentioned, reptiles don't sneeze and cough, so this method of transmission probably doesn't play a major role. That leaves the other major route of RI transmission -- direct and indirect contact. The infectious microbe comes from the respiratory system, out mouth, and into the environment. Anything the snake's tongue touches or the oral secretions drip on is potentially contaminated. I have yet to meet a snake who only sticks it's tongue out in the water bowl.
If it makes you feel better to take water bowls out, go for it. However, I would not expect it to be an effective means of preventing transmission of respiratory infections between breeding pairs.
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