Those may well be ventilation ducts, because the ship, (a reproduction of an 18th century frigate named the HMS Rose, now renamed the HMS Surprise) is now on display moored at the San Diego Maritime Museum, and it's probably for the comfort of visitors in the summer.
I do believe that "Artilleryman" may be one of the 'collectors' mentioned in this Wikipedia entry for "Master and Commander: The Far Side of the World." Do any corrections need to be made to this text, Norm?
(Sound designer Richard) King located collectors in Michigan who owned a 24-pounder and a 12-pounder cannon. King and two assistants went to Michigan and recorded the sounds of the cannon firing at a nearby National Guard base. They placed microphones near the cannon to get the "crack" of the cannon fire, and also about 300 yards (270 m) downrange to record the "shrieking" of the chain shot as it passed overhead. They also recorded the sounds of bar shot and grape shot passing overhead, and later mixed the sounds of all three types of shot for the battle scenes.
For the sounds of the shot hitting the ships, they set up wooden targets at the artillery range and blasted them with the cannon, but found the sonic results underwhelming. Instead, they returned to Los Angeles and there recorded sounds of wooden barrels being destroyed. King sometimes added the "crack" of a rifle shot to punctuate the sound of a cannon ball hitting a ship's hull.
