Do ninjas only get their number when they attempt to become a Chunin?

Done as soon as the graduate from the Academy.

Otherwise it would be called a Chunin Registration Number if it was done the way you think it is.

OK... just wondered why Lee and Naruto had only less than 40 difference, I think... And explains why Haku dont have a number.

Think about how big Naruto's graduating class was. Then remember that even if they didn't pass their jounin's test, doesn't mean they still aren't ninja.

Then include however many people in Lee's year that turned in their papers after he did.

Boom, instant difference in numbers solved.