In the mornings we reviewed the Navigator to determine which activities they were going to do. When the activities were over they checked themselves out and met us where we'd determined to meet. They enjoyed the freedom of not having to wait for mom or dad to come get them, and so did we! Not once on either cruise did we have a problem with our boys checking themselves out at a time we'd not already agreed upon. We know this because the lab paged us when the boys checked out, together. Occasionally we would let them go to a movie together without us, and on our most recent cruise our middle son would sometimes go to Ocean Quest (which does not sign in or out- it is purely drop in), and would stay in there until the time we'd agreed to meet.
I don't let them even go to the park alone at home, but checking themselves out and going up 4 flight of stairs to meet us on deck 9, or down 3 flights to meet us at our room was perfectly acceptable to us. They were together, and are very responsible kids (they know we have HIGH expectations of their behavior, and they've yet to do anything that would make us not trust them). If and when they ever do break our trust... we'll have to re-assess our game plan. I know as a kid I didn't do anything I knew my parents would not trust until I was out on my own at 18, and by then... they may have to pay for their own cruise!