Our youngest was just shy of 14 on our first cruise so we've never done checking in/out of the clubs.
I will say, tho, that at the parks it was a step by step thing for us. We didn't show up on one of our trips and suddenly it was "go for it". It was steps over years. Hubby & I would allow the boys to shop in the same store as us but they couldn't leave. They had to stay together. Then we would sit out 2nd, 3rd, 4th rounds on E:E and let the boys do those alone. We'd allow them to go to the game room at our resort on their own & back to the room. Next we moved to a few hours off from us together in the same park. Then we left them in a park to hit a few more attractions while we headed back to the resort ahead of them. I think it was the trip when we went on our first cruise that we finally allowed them to go places alone at WDW as long as they kept their phones handy & let us know (via text) where they were & what they had planned. At 15 yrs old my oldest son made himself a solo dining reservation with the Yacht Club concierge & treated himself to the clam bake completely solo. Paid his own dinner bill and tipped his server all on his own. That was cool.
So now on the cruises we don't give our boys a curfew. They have to eat dinner with us and keep their Wave phones handy. No going in other staterooms. Nobody comes in our stateroom. Without our prying they will check in with us periodically or randomly join us for shows or other meals. Our youngest (now 15) is a night owl so its not unusual for him to stay out until 2 or later. One thing I do love about the cruises is how it allows our teens to fly solo.