My "chicken house" is pretty small. My hens only go in to sleep and sometimes lay (if they aren't laying in the haystack or potted plants). I have more hens than will fit on my one roost. So they sleep in and on the next boxes. I just scoop out the shavings every couple of weeks and put in new ones. They don't seem to poop in them a lot. If they were in a big nice coop like some of the ones on BYC I would prob rather that they didn't sleep in the boxes. But then they would have more roosting space. I just don't worry too much because, like I said, they only go inside at night. The "house" is in a huge run and the food and water is out in the run. I guess I typed all of that to say that unless it really bothers you or your eggs are nasty from the poop, it doesn't matter if they choose to sleep in the nest boxes.