I also have a theory on this. Its very similar to other's theories in this post, but mine is a bit different I guess ^^
When Sora struck himself with the keyblade, 3 hearts were released. His own, Kairi's, and Ven's.
1) His own heart was turned into a heartless.
2) Kairi's heart returned to her own complete body (it did not turn into a nobody)
3) My theory is that Ven's heart returns to his own body in the Chamber of Waking, and became Roxas.
My thoughts are that the reason why he is generally thought to be Sora's nobody is that everyone knew Roxas could wield a keyblade. They also knew that Sora became a heartless. Put two and two together, brought the mistaken thought that Roxas is Sora's nobody. Xemnas was probably searching for Sora's nobody since he learned he became a heartless. Then he found a boy named Roxas who can wield a keyblade and has no recollection of his past. Seems like a perfect fit right? This is why Xemnas gave him the name "Roxas" (note that the name of the org members are their somebody names plus an X. Sora + X = Roxas. Just wanted to repeat that little fact for emphasis ^^). Xemnas was only mistaken.
Sora's body and Soul on the other hand, became Namine. I have a reason why she looks like Kairi and joins Kairi in the end of KH2. Recall back to the paopu legend "When two people share one, their souls become intertwined. Becoming a part of each other's lives." Sora and Kairi hypothetically shared a Paopu fruit. Therefore, Sora and Kairi's souls intertwined, becoming one. And when Sora lost his body and Soul, Namine inherited SoKai's intertwined soul. Being able to join with Kairi because they share the same soul. In turn, Namine would also be able to join Sora because they too share the same soul.
Now before people are "like but Namine has Sora's body, how can she enter kairi!?" Remember, Sora obtained his own body back right after he became a heartless. Meaning that Namine's body is merely a shadow (as explained in the secret ansem reports). Her entire existance is a shadow, but essentially, she is composed Sora and Kairi's intertwined soul.
Now here's the question of "if Roxas isn't Sora's nobody, why did he have to return to him?" I have about 3 reason for this.
1) His heart may be too unstable or incomplete to be able to live on without Sora's heart.
2) He was connected with Sora's heart for so long that His heart became dependant on Sora or vice versa.
3) Without Roxas/Ven's heart, Sora may not be able to wield a Keyblade.
I'll elaborate on the 3rd one.
Lets look at Riku, the reason why he has a keyblade is because he was chosen by Terra. Terra passed down the Keyblade legacy to Riku. It seems to me, that the keyblade doesn't necessarily choose for itself. But instead, it is passed down from master to master. If this is correct, then why does Sora have a keyblade.
Well. . . Sora does have the heart of a keyblade master connected to his own. Can this be the reason why Sora has the keyblade? This is my theory.
So ironically, according to my theory, Roxas/Ven is the reason why Sora has the keyblade, other than the general idea that Roxas has the keyblade because he's sora nobody.
Unless the keyblade really did choose Sora, then my theory is void.
Well, this is all just speculation, theories, and hypothesis. I'm not very well versed in the Kingdom hearts universe, but this is my theory. I hope this is all explained in KH3. If its isn't, then Nomura is screwed because the events of KH2 made little sense.
* I like emphasis. So don't be angry with all the font decoration.