You have absolutely no grasp on how the Kingdom Hearts universe works, and it's disappointing.
That's because they weren't empty shells. We have seen that a heart can have great effect on someone's appearance, being that, just having MX's powerful heart in Terra turned his hair silver and his eyes gold. Imagine the effect a heart could have on an empty shell that has no heart. That is the whole thing going on with Roxas. He has Ven's heart inside him which changed his appearance.
For another example of a heart being in an empty shell and completely changing their appearance, consider how at the end of KH1, XH took over Riku's body and sent his heart to the dark realm. This means that "Ansem, Seeker of Darkness" was XH and Riku's body and he looked EXACTLY like XH.
It's seriously not that hard to understand that Roxas has Ven's heart, three games now practically go out of their way to say "HEY LOOK, HERE IS THE ANSWER".
There are many possible explanations. The fact that her somebody is still an active force could be one, or the simple fact that Nami is barely even a Nobody, being such a mindfluff of an existence that even Ansem the Wise didn't know how to classify her. Using Nami as an example for anything is pisspoor because she is practically an exception of an exception to a rule.
You should go back to how you original thought then, because it was actually right.