We've only seen flies when things are wet. There has to be a sustained source of moisture, whether from droppings that don't either dry out (dry sand) or get covered and decompose (deep litter). Or from trash, compost pile, spent bedding mounds, water leaks, clogged drain field, or ground with poor drainage and organic matter in it.
We live next door to two big farms with pigs, cows, and assorted livestock. They tend to bring a much, much heavier fly load than my horses ever did. So, we have to take measures to protect our property by keeping things dry or the flies would be over here in a matter of hours, like they did when our grey water drain field got clogged. They got in the house, it was horrible (Tip: those clear sticky fly traps you put on the window near the sill are awesome).
But from our normal chicken situation? We don't get flies.
Planning ahead for how you will manage moisture is essential.
Anywhere they congregate and poop a lot should be covered from rain. So
, a small run should be covered, a big one doesn't have to be.
More space for fewer chickens goes a long way towards keeping things clean(ish).
Build on reasonably high ground away from areas water could linger
, causing the dreaded chicken poop soup.