David,
I always go through this sort of sole searching when I wax a gel coat surface. "What will this do if I ever have to refinish the gel coat?" I ask myself. Of course, the wax provides some protection to the gel coat and maybe puts off the day I'll have to refinish it. It looks good so I wax it. Varnish isn't as porous as gel coat so I wouldn't be as concerned with penetration. A good dewaxing before you refinish should get rid of the wax. I agree the protection provided by the wax is worth the effort.
Geo. C.