In the German tradition, mortises cut into the bottom sill are cut with a special angle at the bottom, with a hole bored down through or out at an angle to allow water to drain out should it get in there. I also know that sometimes the ends of joints, in the mortises or what have you, were sealed with wax or sometimes with paint, but I believe in normal practice they were not. It is worth noting here too that in this tradition the timbers are fully sealed with a mixture of linseed oil and blood paint, and never left bare.
