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Alan, the boatspeed and depth transducers are often combined in one unit with one cable feeding them, so I would guess that IF your setup includes windspeed (always a sensor aloft by itself) and speed+depth, that one connection is for windspeed up the mast, while the other is for a thru-hull transducer for the pair.
Just an educated guess--since I don't know that rig. You'd have to check the wiring you found, see where it goes and what's left at the other end to try checking that. Although, if there's a marine electronics dealer near you that used to carry their stuff, sometimes asking for the oldest guy in the shop will bring about some hints. :-)