"Is this chair free?" would not ordinarily be misunderstood, since presumably you and your interlocutor would have the empty chair before you (or beside you). The usual US idiom, however, is "Is this chair *taken*?" If on the other hand you were asking where you might find a place to sit, you would probably ask "Is there a chair free anywhere?" In a commercial context "a free room" would indeed imply that no charge is made for the room. This implication may be avoided by postpositing the adjective; you might be told: "There's a *room free* in the house". Again, however, a different word would be more likely: "There's a room *available*". In a non-commercial context, where there's no ambiguity, *free* is acceptable: "If you need a place to crash we've got a room free." And if you're asking for a room either would serve: "Do you have a room *free*?" or "Do you have a room *available*?"