Don't stress about it, if you're worried. All domestic animals are quite attuned to our reactions and our stress often becomes their stress since if we're stressing it usually means they have good cause to as well!
I have built onto (and within) coops with chickens in them and never had any issues. This is with broody hens as well. They are quite curious about it, for the most part. Very rarely does one take a fright.
Mostly, I have trouble building because roosters and hens stop freeranging to come and investigate the new nests I'm making for them, getting under my feet and occupying bare boxes etc that I've not even fastened into place properly, strolling into and out of cages I'm making, even perching on logs I'm carrying or trying to secure. Some even sit on my shoulders or head when I work, if I let them. They quite enjoy it when I build and hang around more often than not to watch; they all seem to like the idea of having the choice between various nesting, brooding and roosting cages. Chooks are generally smarter birds than given credit for and will quickly calm down when they realize the banging, drilling etc does not represent a threat to them.
There are some foods you can feed to settle their nerves. Rolled oats are a great one. Poppy seed is also great, if you get a loaf of poppy seed bread or yoghurt or whatever, and give them some treats to work on while you work, will probably help. Any food they love will take precedence over your banging or whatever.
I definitely wouldn't work at night, though, that would disturb them quite badly in all likelihood.
I don't know how flighty your birds are but talking to animals, even wild ones, is surprisingly helpful. They can ascertain much from our tones. Just like we don't need to speak animal to understand an angry noise or a happy one when an animal is making noises at us. Chances are there will be some carrying on, but don't worry about it, some birds just love the sounds of their own voices and others love inciting panic. Some just like to raise the alarm, even over trivial things.
Anyway, long story short, it won't harm them, and like any other animal they can get used to all manner of unnatural noises. Overprotecting them from such human-made stimuli is probably more cause for stress than exposing them. Even wild animals can get totally blase about all manner of artificial noises. As long as no harm comes to them they will get over it and get on with their day.
Best wishes with your building.