For some reason, I doubt that Ventus' heart did remain in Sora's body. For one thing, Ventus' heart was/is on the verge of death (Or rather, about to return to Kingdom Hearts) MUST merge with Sora's heart if to sutain an existance. Its very likely that Ven's heart only established a connection with Sora's body and cause it to appear like Ventus while Roxas would use the connection with Ven's heart to "access" emotions and "store/retrieve" his memories. (Which was what Vexen was referring to when he mentioned "The other side" of Sora's heart.)
If its been stated explicitly in the BBS Ultimania that Ven's heart stayed Sora's body, never mind...