I've been trying to figure out how to respond to this without rambling too much. Everything I'm going to say is my opinion or personal preference. Others have different opinions. I don't try to micromanage my chickens but try to let them be chickens as much as I can. I understand that we all have different goals, set-ups, management techniques, weather, flock make-up, and so many different things. What works for one may not work for another. I try to provide predator protection and cover basic needs but leave as much to the chickens as I can. Let them do the work.
Dad had a flock much like yours will be when those chicks grow up, one rooster and 25 to 30 hens. Most slept in the hen house but some slept in trees. Occasionally he'd have one that slept in a hay barn. They free ranged and practically all the eggs were fertile. It did not hurt them to sleep apart as far as them being chickens was concerned. When they were out free-ranging they did scatter quite a bit. Since the eggs were fertile I don't know why that would be an issue.
I don't see anything wrong with them sleeping in different coops. It will not hurt them. The issue is that you probably can't control where they sleep. You can build a new coop for them and maybe train them to sleep there, but some or all could decide to move to another coop.
I don't know what our current facilities look like, size or how they are laid out. Any runs or total free range? Not sure what I'd do in your situation. Even if the coop is too small a large number may try to crowd into one. As long as they do not hurt each other I don't see that as a huge problem. My first though is can you enlarge one of the current coops so it can handle all of them? If you have a decent sized run you could train them all to sleep in there. That might make your life easier. But for the chickens, I don't see how it hurts them to sleep apart.
