Hard drives are not shipped anywhere near a clean room env. The inside of that box is probably one of the cleanest places on earth. It even blows other clean rooms like space craft manufacturing facilities out of the water.

And you're missing the fact that the outside of the box isn't a clean room, and it has to mate with the clean room at the customer facilities. A bajillion baggies of parts is a non starter if the outside of those baggies isn't a clean room env.