In Kh'Days, it's specifically stated by someone that Xion is a Replica of Sora's Nobody. The words "Sora's Replica" and "Replica of Sora" do not exist in the game.
But it's Sora's Memories she was absorbing, less so Roxas's, thus making her a Replica of Sora. Note at the end of the game, her looking like Sora and stating that
this is what she was to become, not Roxas.
As for Xemnas' encounter with Sora, I'm pretty sure that was done in order to test Sora's power. Besides, I'm Xemnas was curious about Sora similarities with Roxas and thus satisfied his curiosity by meeting with Sora.
Any connection between a Replica and the origin has to start from somewhere. Repliku's started when Vexen fought Riku and took the data - whatever that's made up from - and implanted it in Repliku.
For Xion to be anyone's Replica, she'd have to have something of theirs. Roxas would have nothing to give - beyond things that belonged to Sora. This ties in with the Final Mix battle and Xemnas passing through Sora in a manner similar to how Marluxia passed through Sora in Re:CoM.
That was the basis, and from there on, Sora's Memories leaked into Xion through Roxas. She was copying Roxas for whose Nobody he was, not for himself.
I'm not saying that Ven's heart and Riku's heart are similar because they are fractured, but rather because their hearts became nearly empty at one point.
I have a hard time taking this since the 'emptyiness' in Riku's case is really metaphorical. Both Light and Darkness remained in his Heart, he never really pushed them out, just denied them. That's why it was possible for him to recover against Zexion the way he did - both Light and Darkness were still inside him, Namine just helped him accept that fact. It's not like he regained anything.
If he really was empty, tampering with his Darkness like XH did would've been meaningless.
As for Ven, as you said, it was never implied how bad his Heart-fracture was, but I doubt it was empty in that manner. More literally shattered.
Ven's memory loss is not confirmed, but if Roxas has Ven's heart, then perhaps Roxas' lack of memories is an indication that Ven's heart lacks memories as well (though this is not necessarily definite proof).
If Ven's Heart lacked Memories, Xion would never have been able to take his form, since her appearance is based on what someone remembers, and her having that same memory inside her.
Xigbar seeing her as Ven = Xion had Ven's Memories inside her.
That is indeed a possible reason for their head clutching, but I personally it is more relevant to Zexion's comment about dark memories, since the head clutching didn't begin when Riku's memory started to play, but instead began as soon as Zexion began talking about dark memories.
It's a very narrow way to look at that scene, especially seeing the overall relations.
Then there's the part where they morph into Sora with saying that 'you destroyed your home' or something to that effect. If you wanna go that metaphorical on that scene, you'll have to explain that too, but I think that's one of the best indications showing the problem was an identity issue. Roxas and Xion are Sora; they shouldn't see that Memory. They do, however, so it hurts.
Also, note the static. It's a clear indication something's wrong in this Memory-playing out. And it's the biggest static yet before Roxas starts clutching his head.