actually its not confusing at all; i believe that xemnas was looking for the LS, not ven in the chamber of waking; he destroyed ven's body, so he wouldnt need it; and i guess he had aqua to see if she knew where he was;
and im guessing for coded, freeing those unhappy souls refers to terra in his armor, freeing ventus from sora, and aqua from kairi;
they made a promise to be together again, and those "unhappy souls will be freed from their torment" by the one who can connect his heart with anybodies and free them from their armors/despair