I have a lot of fox squirrels where I live. The fox squirrels have nests in the trees in my back yard. We made a feeding station for them with sunflower seeds. They go by my coop, run and range area all the time and barely look at the birds and the birds could care less about the fox squirrels, but the gray squirrels I chase off as they get into everything, but I have never seen them bother the chickens either.
I have a whole bunch of old nut trees from walnuts to hazel nuts to horse chestnuts and therefore a ton of squirrels. I was worried because squirrels were getting in through the vent in the top of my coop and burying nuts in the bedding. As soon as I moved 2 chickens out there though they stopped. Now with 11 chickens in the coop they avoid it. I haven't seen signs of a single one setting foot inside. They don't seem to bother chickens or even their feed.