I would render a guess that the noise you may have been hearing was the propellers rising up to sea level since the seas were choppy. This is not unusual especially for an older vessel. The stabilizers can only do so much in rough seas but imagine if the ship didn't have any at all!! We did a Bermuda cruise from N.Y. back in 1992 during October when there was a hurricane swirling south in the Caribbean. Even though the storm was so far away, the seas were very high. This sailing was on the M/S Meridian (Celebrity Cruise Lines Flagship) and because the ship was built in the 1960'2, there were no stabilizers. Needless to say, the ship was mostly empty as you experienced. Thankfully, I don't get seasick ;)  Bon Voyage.....