another way to put it would be: What the number..what's the number of students..? I hope it helps.

As Lindsey has noted, we cannot say "what thousand" in that sentence. To be honest, we would just say "how many students are in your school", as it cannot be assumed that the number is in thousands. I guess Chinese schools all have a lot of students :)

No. How many students are in your school? How many thousands of students are in your school? Good luck!