All three did you go, have you been and had you been seem okay to me. However, I'll try to tell the subtlety I find.
Firstly, I'd select the verb been over go. That's because have/had been refers to go to a place and come back. In the context of visiting a place, been serves better than go. But that does not mean the first question is incorrect. A note for the first question though - when you and the listener are talking about the same spot, it'd take the definite article the.
In an informal speech, you may ask
Did you go to the picnic spot (which) you were asking me?
This means you are asking whether the person went to that place.
Had you been to that picnic spot which you were asking me?
Looks okay (using that instead of the talks about the same spot, so article is omitted). But then using had gives a flair of more past and not recent past.
Have you been to that picnic spot which you were asking me?
Also looks okay. Just using have here I think talks more about the recent activity. It may seem that he has just visited the place and you are asking this. Using have + participle is recent as compared to had + participle. Compare I had done this over I have done this. The latter is recent past or at least its effects has remained as on the time the sentence is spoken. Good to note that in your very own question you used "....I had
have visited long back." That supports it!
But as I said, all three seem okay to me.