Actually it is a bad thing that all the money was returned. You see, one of the aims of this exercise was that only part of the money would be returned. The rest of the money would be assumed to be black money. Now if the entire money comes back, then the assumption is that there was no or very little black money.
Now they need to look at the deposits and see if there are any discrepancies. It is possible to figure out which are the fake accounts but it will take time. And this is another reason why they need to limit the withdrawals - because if they remove the limit, then all the money that was in the fake accounts can be withdrawn immediately and the whole exercise is futile.
That said one benefit is that the banks have a lot of cash and this is ideal for them because they were sitting on a lot of NPAs. This also makes the government job of having recapitalize the banks easier. So in all there are benefits but it remains to be seen how the government are going to spin this.