Actually deposits in Jan Dhan accounts are hardly significant when you compare it with the total value of old currencies. Till the first week of December, the total volume of deposits (after demonitisation) in Jan Dhan accounts was merely about 30,000 crore. I am sure many of these accounts were used to deposit black money but in the larger context that is a very small amount. If you subtract the genuine deposits from 30,000 crore I am not sure if it is even worth going after 25 crore Jan Dhan accounts.
Edit: the livemint article you posted says that about 44,000 crore have been deposited in 45 days. The numbers are consistent with the above data.
http://economictimes.indiatimes.com...s-hardly-significant/articleshow/55792611.cms
http://www.ndtv.com/india-news/jan-dhan-deposits-stabilise-get-rs-1-487-crore-in-7-days-1633957
Also the deposit limit in Jan Dhan accounts is just 50,000 rupees. So even with a 10,000 a month withdrawal limit the money will be out of the system before the already stretched IT department gets to examine thoroughly.
It is also worth mentioning that Jan Dhan accounts are owned by the extremely poor class who don't have a bank account otherwise. Suppose I am one of them and I somehow managed to deposit 40,000 rupees in my account. What is the IT department going to do exactly? Almost none of those people have any genuine employment contract. Are you going to jail them, drag them to courts? Send IT notices for 40,000 rupees? It is next to impossible to do anything about it.