Definitions of "poetry" and "nonsense" aren't the issue.

If Colcord were going to create a new rhyming line for Whall's couplet, she could have done a lot better than the seeming non sequitur of a river having topsails.

My guess is that she printed what she'd heard.

But as nonsensical as the stanza might look on the page, it might have sounded better at sea. The improvising shantyman, hurriedly looking for a rhyme and not concerned with pleasing imagined readers, may simply have changed the subject between the lines. The "she" in line two would then refer not to the Missouri but to the ship.