Yeah, I'd guess they were sleeping in the higher ones. They instinctively like to sleep as high as they can get.
I'd go ahead and open the lower ones and make sure a fake egg is in there. If they are still sleeping in a lower nest, I'd move them to the roosts at night. They should soon get the message.
I always want the nests open when they start to lay. They are creatures of habit. If they get used to laying somewhere else, it can be hard to break them.
Don't freak out if you first egg is under the roost or somewhere else in the coop. When they first start to lay, a lot of them seem to be surprised by the process and might drop their first few eggs about anywhere. But as soon as they gain control of the process, they look for a nest to lay in. A lot of them do lay that first egg in a nest to start with and most lay the first controlled egg in a nest. Those fake eggs do help.
Good luck! It's about to get even more exciting for you.