Its an American thing, the British used to Nod their head. They were smarter than to take their hands off the bars. Indian Motorcycles in the 50s fostered a brotherhood type thing where you would wave to acknowlege your brother Indian rider. It just spread from there. Nothing special about the development. It became almost mandatory in the 60s because " You meet the nicest people on a Honda".
We could make up some mysterious reason here! Spread the story through the web and I bet in a few years it would be taken as fact lol.