Raytheon Bidata ST 40
SOG is a completely separate measurement from the speed reading given by the paddle wheel and knotmeter. Usually it comes from the GPS and is fed into the seatalk bus via an NMEA interconnect at the autopilot.
The CAL factor *will* definitely adjust the speed shown by the knotmeter, unless of course something is wrong with the ST40 instrument itself.
The only time you need to revisit paddle wheel placement is if you get significantly different speeds reported one tack vs the other. Provided it is in relatively clean water and turns freely, you should be able to CALibrate it to read accurately.