I have only 10 deer so far, they come for their goodies each evening (apples, carrots, bread, etc.),that's the time I spray them with permethrin or get Ivermectin pour on if possible. The tame ones that I can pet get spot on stuff for dogs, like frontline etc. It helps to keep all bugs/flies off of the animals. I figure, if the bugs stay off my deer, they are less likely to catch disease. No standing water in the pens, they get fresh water in buckets as needed, always rinsing buckets out well. So far, I've been blessed, no disease here, though I have a creek running about 40 yards. next to the pens. I don't like the thought of spraying the pens, would be wasted money to start with as it has been raining quite a bit the last while and insects might get resistant too. At times I spread lime though, helps with smell, bugs, and fertilizes.
Hope this gives you some ideas.