Lighter:

You asked, "Why use an "obscure hidden meaning" instead of the literal reading of the words?"

First: The song is comic, about tongue in cheek punishments for the erring sailor.

Second:
In a real-life naval situation, the captain might not even have a daughter. If he did, she probably would not be aboard. If he did and she was, the drunken sailor might, on the surface, see putting him to bed with a female (ANY female) as a reward rather than a punishment for his drunkenness. Alternatively, the captain in that case would surely be enraged, and not only the drunken sailor but those who instigated putting him in her bed would be severely punished. All of which would be in conflict with the spirit of song, as in the first commend.

Third:
As a parallel to "kissing the gunner's daughter", which is traditionally known to have the "obscure, hidden meaning" of being flogged with the cat while bound to one of the big guns.

q.e.d. Which should have been obvious.

Dave Oesterreich