I think that in a well managed DL, the good organisms outweigh the bad guys, so there's a healthy balance. Also, there have been studies done regarding the benefit to chicks that are raised on deep litter, whether it's the typical composting litter, or shavings that are continually topped off, rather than being removed and replaced. Those studies have shown that subsequent broods of chicks actually benefit from the microbes left behind by the previous clutches. They grow faster, exhibit better feed conversion rates, and the mortality rate is less. The theory is that they have a stronger gut flora, and some of those microbes actually produce B vitamins which enhances their growth.
My take away from all of this is: if doing conventional brooding, keep those shavings dry. If using shavings, I tend to top them off, not change them out unless they get wet. I also get some soil into my chicks during the first 2 weeks after hatch to take advantage of that 2 week window of opportunity provided by the antibodies inherited from their mother.