For hatch seals, rudder lines and rudder area, I use a spray on Silicon. After the carrier evaporates, there is no sticky residue and no build up. It doesn't last long, but seems to work well. I think there are much better Drive lubricants. I agree with JimL that some of the silicone carriers can be drying and detrimental to some surfaces. I haven't experienced any problems with these applications though.
The concern with WD-40
with your application is that it leaves a gummy residue which does not rinse off. This can build up, attracting small particulates from the water which can end up being abrasive.
Here's a discussion on different lubes:
http://www.hobiecat.com/community/viewtopic.php?t=6308