How many stones are in the garden seems to make sense to me; there after are isnt needed
I think that that would be a different Polish verb; "są" instead of "masz".
In English the word got in this sentence is not necessary. How many stones have you in the garden would be perfectly acceptable.
I think it might possibly be Welsh. "how many do you have...." (now the main answer) is also the most usual way of phrasing this question.