Kyon's name is one of the most well-kept secrets in SHnY. A more well-kept secret than his name would be only... Kyon's sister's name.
But I wouldn't be surprised if in the last novel there was a dialogue between Haruhi and Kyon like this:
Haruhi: By the way, Kyon, you've never told me your real name.
Kyon: Hm, and why do you want to know this now?
Haruhi: I was just asking, you don't have to tell me if you don't want it, silly.
Kyon: It's Watanabe Tomoya.
Haruhi: Watanabe... Tomoya? Such a common name! That's not funny at all! I, as the leader of the SOS Brigade, order you to change it to something more interesting!
Kyon: You wish! That's been my name my whole life, there's nothing wrong with it! Do you think you can simply go and start changing people's names now!?