I've never seen long lines for the AquaDuck while the ship is in port, but then again I always cruise in September when the ships aren't very full to begin with. I imagine if you cruise during a busier season, you might have longer lines.
The AquaDuck is open when the ship is in port, provided the weather conditions are safe. If it's too windy, they will only allow double riders (no single riders) and if it gets too bad, they close the AquaDuck completely.
I know my parents tried to go on it while we were in port in Nassau, and it was closed due to wind conditions. So even if the Navigator says it's open, it's not guaranteed to be open!