Having one line about sleeping with the captain’s daughter might have been even more amusing (and thus more catchy) because of the double meaning.

Very likely, probably why the whole captain’s daughter = captain’s whip thing took off as sailor slang to begin with.

your average deck hand singing sea shanties isn’t thinking metaphorically when he’s singing about getting drunk and laid.

I never claimed it was a metaphor, it’s slang. Similarly, the “gunner’s daughters” were the gun barrels midships on gunships.

And insisting that the one line in the song isn’t about fucking is feels like wishful thinking

I mean, no skin off my nose if you believe that, but it seems pretty clear judging from the fact that the captain’s daughter is a well known slang term for a whip in a song about punishing a drunk that that is at least the correct original intent. Of course anybody can interpret anything any way they want.