If you can answer this question you definitely have OCD.
And what do you have if you ask someone this question?
A bizarre interest in other people's gardens.
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".
or perhaps how many stones are in the garden?
"Ile kamieni jest w ogrodzie?"
In English the word got in this sentence is not necessary. How many stones have you in the garden would be perfectly acceptable.
Added your version.
Is this from a British dialect?
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.
or Scottish English
Wouldn't the most usual way include "in your garden"? Or are two children (siblings) comparing their stone collections?
I agree, changed to "your" now.