There are restoration shops who wouldn't dream of using plastic filler too.
You are right though, the shim should be a last resort. I know I bend hinges to correct it too, however when a mistake has been made and the car is painted and done, a shim properly placed just isn't that big of a deal. As I have said, the car has STACKS of shims to make fenders fit at the factory, STACKS I have seen a half inch of shims on original cars. So a neatly placed shim to make your hood or trunk fit perfect just isn't a big deal. When I put my hood back on after having the hinges powder coated the back was high for some reason, I couldn't adjust it down without removing the hood and hinges to hog out holes or something so lowering it with a shim was fine with me.