Well he can definitely tell the difference, but it's possible that Xemnas knew of Ven's heart being inside of Roxas.
Of course Xemnas can tell the difference, there are several indicators of this:
1. He was frantically searching for the chamber of Waking, which houses Ventus' body and soul, and actually never goes beyond making
references about Ventus to Roxas, never designating him actually
as Ventus. Xigbar does the same sometimes btw, in some scenes/secret reports in Days.
2. Xemnas was entirely indifferent towards Roxas in any regard that would go beyond the usefulness of Keyblade wielding and would have gladly gotten rid of the kid if it would have meant that Xion could have become a full Sora clone.
3. He didn't have any qualms to order Roxas be eliminated when he deserted the Organisation.
Yep, that he knew that Roxas had Ven's heart is almost silently confirmed since Xemnas has also memories of MX he knows about the "hearts shape the appearance"-bit.
I would also assume that Mickey got his hint as to where Ven's heart is from seeing Roxas in the end of Coded, realizing his twin-looks to Ven and from there deducing that if Sora's Nobody looks like Ventus, his heart must have been involved, therefore stating to Yen Sid that he may be "close to finding out where Ven's heart is".
Probably MX; Terra shouldn't be aware of Ven's slumber after defeating Vanitas.
It can also be a mix of both, as Xemnas has memories of both Terra and MX.
Ventus also fell asleep three times.
First time was four years before BBS when MX shattered his heart for the first time to create Vanitas, second time was when Terra asked him some questions when he first came to the Land of Departure when his heart was still not fully re-formed and the third time was when he destroyed the X-blade and Vanitas along with it.
So it can really go either way or a mix of both.
Judging by how Xemnas acts in DDD and how his plans unfold throughout his career as the Org's superior, I'm certainly on the impression that there is much more "Xehanort"-influence on Xemnas' new mind than there is "Terra"-influence, which shines only through in small vibes.