I checked my SN today and find no 5A fuse (or any other small size) in the low voltage wires to the windlass. I only have the 100A breaker in this picture.
--The fuse holder to the upper left of it is something I added for a Caframo fan in the forward stateroom - nothing to do with the windlass. I believe the heavy cables you see heading aft through conduit up high are going to the "Mat" and "Bome" furling relays in the head, so nothing to do with the windlass. On my boat there are two holes through the forward bulkhead - the one on the right carries only 3 wires for the genoa furler and the one one the left carries the windlass wires plus some other wires that seem to be running lights, maybe chain counter and low voltage switch wires for the windlass.
Sorry not to be more definitive, but hope this helps a bit.
Best regards, Craig
SN68 Sangaris, Tropic Isle Harbor, FL