Why people think he had known him beforehand? I think the following qoute by my friend clears the misunderstanding very well:
"I don't think Naruto knows who Shin is, when Sasuke told him about an uchiha he didn't knew anything.He said "it's you" because Sasuke informed him about a new uchiha and he realised that the one in front of him it's the one Sasuke told him about."