You counter balance the rudder the same as the other surfaces. It doesn't have anything to do with the aircraft and it's surface being parallel to the ground. On a full scale aircraft you would remove the rudder from the plane, place it in a jig that uses the hinge bolts, positioned so that the surface of the rudder is parallel to the ground. Now with it in this position you use lead, brass, etc to balance the rudder to the recomended amount. Place the rudder back on the plane.
For RC planes it's a bit easier.

You are right though, in that the counter balance is more for aerodynamic effect than balance on an RC plane. I think the kit makers use these for looks more than anything else, or the fact that the full scale version has them so they use them on the model plane also.
I have seen very few kits that had weight balances or give instructions on balanced surfaces.


Bill