"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).
Another common US idiom, which avoids the problem, 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?"