Studies of commercial flocks have shown caged birds to be the healthiest. Insects, worms, wild animals and birds, can carry bacteria on their feet, bodies and fur, and in their droppings and saliva. Sharing ground, eating them, and eating or drinking from the same reservior can play a role in fowl cholera, pox, infectious bursal disease, mareks and probably many other diseases. I would think may also be more likely to get into natural or created toxins/poisons. Having said all that, I still like to give them a little free run time every couple days.
As far as predation, that just depends on where you live. I have coyotes, dogs, hawks, birds, raccoons, skunks, and bobcats. I have to cover my pens with chicken wire, twice on the sides and once on the top,and bury it 6 inches into a trench, followed with fence post cement and a base board. A neighbor had a bear tear the door off his henhouse. After he replaced and reinforced it, the bear came back and tore the siding off. He's out of chicken raising.