See
herefor Michael Quinnion's take on this, although I believe other sources give Davy Jones as a corruption of the name for the Devil and Jonah, the lad that spent three days in the belly of a large fish. When a ship crosses the equator a bizarre ritual is enacted where, amongst other things the smallest sailor aboard dressed as the devil. That may be relevant. Maybe Jones was a Welsh sailor of antiquity who, suffering from vertigo, terminal clumsiness ad an inability to tuck his blank into his blanks, kept falling overboard.