Ventilation removes ammonia fumes from the coop. Unless you sit there all the time, ready to whisk each plop of poo away to the compost pile the moment it comes out of the chicken, there will be some ammonia being released into your coop's atmosphere. It does not take all that much ammonia to cause subclinical damage to the tissues of the chicken's respiratory tract, which makes the chicken more vulnerable to any respiratory 'bugs' that may be floatin' around the environment. Basically if your nose can smell ammonia, there is enough of it to be harmful to lung tissues.