I was surprised to see in the Oxford English Dictionary that the first recorded use of "cherry" in the sexual sense dates only to the early 1900s. As Bruce pointed out, the "Riddle Song" is centuries older. So T.C.'s version very probably is fairly recent.

I tend to think that taboo versions are the "real" ones, which somebody later cleaned up. I easily forget that love, riddles, and trying to get the baby to sleep are as basic to human nature as ribald jokes are.