1. and 2. are synonymous, and 3. and 4. are synonymous.
'before' is implied by the use of the perfect structure 'have been'.
Q: Have you been there (before; i.e., in the past)?
A: No, I haven't (been there (before)).
A: Yes, I have (been there (before)).
With 'yet', the speaker assumes that you made plans to go, and s/he wants to know if you actually went or not.
Q: Have you been there, yet?
A: No, I haven't (been there (yet)).
A: Yes, I have (been there). *'yet' is not required with a positive reply.
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