I always have trouble with sentences which imply the "you" - esp. when we don't have the context around this sentence. "Are there clothes?" should be acceptable too.
I agree with you. 있다 does not mean "to have", it conveys the idea of "to have", but it means "to be". In a context whers you talk about a store and someone asks "옷이 있어요?" it would definitely be translated as "Are there clothes?"
To be in the sense of existence...
I have some at home. I just didn't bring any to Korea.
있다 means to have/to exist or as nleconte said to be in existence....
이다 means to be.
너는 옷이 있어요? Isn't this more direct? 옷이 있어요? I would think this is asking are there clothes like. 맥주 있어요 do you have beer?