To get the pokeflute in Heartgold and Soulsilver, you must go in the Kanto region and must be able to use the radio in the Pokegear in Kanto and when you use the radio, put it all the way on top.
it has no meaning to it. It's just like poking someone in real life.. people may do it to let you know they are thinking about you.. to say hi.. or just to poke.. i dont know. Why do you poke somone...