How long had you been married? is actually the pluperfect/past perfect which is to say, it is normally only used when combined with the past tense. How long had you been married before/when you got divorced? As such I would say the more common way to say it in English is How long were you married for.

The first is more proper English, but the second certainly is used and would not be considered incorrect. The meaning is the same, but with the first you have the option of continuing with a phrase eg. "How long had you been married when your wife had the affair." Using your second example sentence in that manner would sound a bit awkward.

Both sentences are correct and mean the same thing. However, the second sentence would sound better if you changed it around a little to: ""How long were you married for?" In English, always start questions with the question word. Also, in English, it is possible to end a sentence with a preposition (for, of, in, at etc.) but only if the meaning is obvious.

Both sentences are correct and they both mean the same thing

They're both correct, but the second one sounds overly formal. I'd more likely say, "how long were you married." They do not mean exactly the same thing. "How long had you been married" WHEN SOMETHING HAPPENED? "How long had you been married when you had your first child?" "I had been married for three years when I had my first child." At that specific time, he had been married for three years. After that, maybe he remained married or maybe he didn't. "For how long were you married" (or, better, "how long were you married") implies that you are no longer married. You're asking about the complete duration of the marriage.