I always thought Snake was just a baby that was abandoned at birth because of Harley Quinn syndrome and just sold off to a freakshow; the circus group found him and freed him from his cage. As for the whole talking to snakes and being affected by snake flutes and such, I thought it was because he grew up with snakes his whole life and didn't get much human interaction, he just got used to the characteristics of snakes. Plus the snakes are his friends/pets and people who've had pets for a long time do start thinking they can 'talk' to their pets. (Like if you had a dog for 10 years, you know signs of want the dog wants even though there's no speech)
Also, Snake has a forked tongue? Can someone post an image of that? I don't remember seeing it! (Plus sad truth is, that in freakshows in those days, people did mutilate actors or beggars so that they could earn more money. Like having a kid loose an arm on purpose so that passers would feel more sympathy and donate more money.