Becasue 1) if they get used to sleeping in there it may become habit and 2) if they sleep in the nestboxes it means poop in the nest boxes and lots of it. And thats means poopy eggs. You want to avoid that and either block the nest boxes until egg laying age and/or make sure roosts are away from the nest boxes and placed higher up.
My main issue is that when they're in there not laying, they tend to poop...then the eggs get all messy. So, we put a flap down over them after laying time is done for the day. Then they all hang out on the roosts and the nests stay nice and clean.