The roosters were probably aggressive, and the hens hid quietly.
Edit: Are you sure it wasn't your neighbors who like to sleep late.
I have two separate chicken coops and in one of them I have 3 hens and 2 roosters. Last night both the rooster were killed (I'm guessing raccoon) and the hens were unharmed. I've had this happen before where just the roosters were killed. Do raccoons go for roosters first? Just wondering