Juan Arturo O'Hara uses a pistol with a silencer. However, the weapon is a revolver, a type of pistol on which a silencer does not work.
Both detective Shayne, agent Juan (and presumably anyone else for that matter) have no trouble entering the ship's cargo hatches and compartments which, as per on-board security regulations, would be locked against any such breaches except by authorized personnel.
If the smuggled diamonds are supposedly going to German factories, why are they smuggled from New York to Honolulu in the Pacific Theater?
Answer, because with the submarine war sinking cargo ships in the Atlantic, it made sense to take the longer route through the Panama Canal and across the Pacific.