Marc, the "Yankee Doodle" reference is conjecture too, but at least we know that YD was "riding on a donkey" and that the song was well known in the 19th century. There's no evidence for the other interpretations mentioned.

My own *guess* is that the phrase in the shanty is more or less meaningless, but that the original singer may have had "YD" in mind when he first uttered the words.

The usual tune for the shanty, however, is the great "Bonnie Laddie, Hieland Laddie," which looks to be a genuine Jacobite song from the 18th century. (Slowed way, way down, Jeannie Robertson used it for "My Son David.")