OK-- moisture in dog's ears causes YEAST infections, usually.
The moisture won't promote infections. Stress on the birds will promote the infection. It doesn't matter what the stress is: it could be heat, cold, new birds, a change in surroundings, starting laying, a change in feed, etc.
Too much moisture is not really much of an issue here--except for those 4 days of rain we might see this monsoon, and then the 2 days of rain we get in January. If you are seeing IB in your flock, it is because it is HOT outside and the chickens are stressed. One chicken goes down with IB, and since all the birds are huddling together in the shade (or in the shade in a damp spot on the ground) they are spreading the IB around like wildfire.
If you have 15 chickens packed into a 5' by 5' space---and they are all stressed from the heat--- and ONE chicken sneezes, they are all going to get it.
SO: go ahead and flood the run. You'll get more flies, but it will keep the chickens cool. Isolate anyone you suspect has a respiratory problem, and make sure your flock has TONS of shade, so they are dog piling to stay cool. ALSO--add ACV to you waterers. It will kill germs, especially when birds are standing (and thus pooping) in the water to stay cool. It will keep the spread of disease down.