will the smell hurt the birds when they roost at night and being in there during the day to stay out of the weather . I have vents at the top of the coop and windows I could open but I don't want then in a draft and get sick .
You don't say where you located (just a general location) or provide more information that would help you get better advice, but if you smell the ammonia your birds are breathing it in, too - and their respiratory systems are even more sensitive than ours. How many chickens do you have in the coop? How big is your coop? Do they have access to a run? Are your vents open or closed? (You mentioned that the windows are closed but I don't know if the vents are too) What are you using for litter on the floor? What are your temperatures running? Where are the roosts located in relation to the windows? How old are your chickens? First thing you need to do is get those vents open if they are closed. It's 0 degrees here in northwestern Wyoming this morning, our exhaust fan cover is open, vents are open, the gable vent is open, and their pop door is open. The only thing I shut down is whatever window might be on the side the prevailing winds are coming from, especially if it's also snowing. Chickens are better equipped to deal with cold when they've been slowly acclimated to the falling temperatures, than they are a buildup of ammonia and moisture-laden stale air, so ventilation and air flow are critical even when our instincts tell us to seal the coop up tight against the cold. Moisture in the coop comes from their breathing, their droppings, and their waterer (if it's in the coop) and needs to get out. If the windows don't allow strong drafts directly on the roosts, get them opened, too. Get some fresh straw, dry leaves, or pine shavings added to the floor! You have more nitrogen than carbon going on in your coop and the ammonia smell is coming from the droppings that aren't breaking down. Composting slows down in really cold weather, so unless you stay on top of it (if you are using any kind of deep litter) the balance can be thrown way off. You need some dry, absorbent material in there no matter what you are using for litter. I don't heat or insulate my coop. Our temperatures have been down to -6 degrees already, and this week is expected to be even colder, down to -14 on Friday. <sigh> Winters here are long, too. We got our first significant snowfall of the year on October 12 this year. The first year I had chickens we had our last snow of the year on June 6th. But I even raise chicks out in the run - no heat lamp - when our temps are in the teens and twenties. I just use a heating pad draped over a frame made of old fencing and covered with straw to form a "cave" for them and they thrive, even just a day out of the incubator. So don't let the cold scare you - be more afraid of moist, ammonia laden air and get that coop opened up.
I don't know what your coop set up is like. But have you tried a poop board with PDZ? The PDZ granules will dry out the poop and take away the ammonia smell. You'll probably have to clean out the coop more often since they're spending more time there in the winter.
Listen to Blooie. I did last year and my birds came through the winter without a problem. Our 1 by 3 foot vents under the eaves are open year round. Also have the pop door open year round into a run that is covered in clear vinyl on three sides. Coop is nice and dry with no nasty odors.
