Marine Tex will work fine for filling the hole in your rudder. I've drilled holes in new rudders, decided I didn't like where they were, filled them in with Marine Tex and redrilled partially through the Marine Tex after it set up and hardened, it it's proved to be very solid and is holding firm. I would caution you, however, against using Marine Tex to fill nicks in your fiberglass hulls. There have been many posts on this forum that say that if you go back over the Marine Tex with polyester based gel-coat (the stuff Hobies are made of) the gel won't adhere well to the Marine Tex, an epoxy based product. Use a polyester based filler to get the best results for repairs on Hobie hulls.
Mark Van Doren
H16 Seabreeze #112205 (Richard Petty Signature Edition)
H14T Fantasia #47787
San Juan 28