Yesterday I recalled a version of the ballad which has one resolution of the puzzle. It includes these lines:
He swam until he came to the (rascal pirate's?)* side.
He climbed on deck and went below: by none was he espied,
And he sank them (etc)

It would be easy enough to bore holes from inside, though important to avoid detection and to get out again before too much water had come in.

*I forget who the enemy is in that particular version.

Richard