Ah, blatant theorizing. How fun...
Anyways, there have been significant discrepancies and mysteries regarding the full nature of the Replica Program, implications which may very well play a large role in 3D and beyond.
The most significant clue of this, to be sure, lies in one of the Secret Reports out of 358/2 Days.
The other vessel? Interesting. We know that this cannot be referring to Repliku, as he was created within the confines of CO, not brought in with Vexen. The question remains of who, exactly, this "no.ii" is.Of nearly equal potential importance is where, exactly, Repliku's heart went.
Could it have embedded itself within Riku? Or, perhaps, it found its way to another part of the castle, to a dormant Journal, thus setting up Re:Coded.
Beyond these three mentioned replicas, it is reasonable to say that there were many other replicas. The magnas go so far as to show Vexen with multiple replicas of himself. (Though, I don't exactly consider the magna canon, personally.) Xion, as we know, was labeled "no.i". How then, would she have been made to the level of perfection we have seen, if she was the first? Surely, there were more, inferior replicas created prior to the Organization going "all in" with Xion. Perhaps these replicas, too, had fully functioning hearts. More likely, though, is that they would be, theoretically, incomplete or broken. Replicas have issues with knowing that they are fakes, as we have seen from both Xion and Repliku. (Possible enemy for Sora's inevitable foray into CO? I like to think so.) Still, the point remains that they may exist, and may play into future games.
Vexen was one of the traitors aligned with Marluxia. That much is clear. If he was in support of an overthrow of the Orgainization, wouldn't he utilize his epic army-building abilities?
Anyways, theorizing over. Thanks for reading, and feel free to rip this all apart with your unforgiving claws of dispute. It is just theory, in the end.