Amuso and Persico apparently still get their cut. Or their families anyway. Obviously Persico has still had a lot of his own family on the street to see after his interests. People write off Amuso but he's still has influence from prison. DeFede flipped because Amuso suspected him of holding out on him when later acting bosses like Crea and Daidone were kicking up more to him. And obviously Nicky Jr. was kicking up to him as well. Though there is probably a more personal connection there, since Amuso and his father were friends and it was Amuso who got Nicky made in the family for his protection.

And while it's true that the guys on the street are content to have the official boss behind bars, that doesn't mean the official boss is powerless. They are not in a position to run things day to day but they often still have a great deal of clout.