An ex army ranger once told me that the 'missing' money in the military budget goes to operations like the ones he was part of, which of course he could not tell me about. Of course there is also waste and pork, but I think the majority of this money is for black ops.
Sounds like he fed you some bullshit. I see no reason why it wouldn't be placed under a generic category with zero information regarding it possibly even lumped into something else. This is how it worked with classified projects when I worked in DoD contracting; not sure why this would be any different.
They're different for sure but the required secrecy is essentially the same. Just because something is a secret doesn't mean it won't get accounted for. Granted the DoD accounting practices are horrific but where they exist it will get counted.
Now, how you can give the data to find corruption without revealing black ops, I don't know.
Case in point are the Stealth helicopters they used in the Bin Laden raid. Up to that point, no one outside the military and probably very few inside the military knew they existed.
A fact that would have been concealed had they not crashed one during the operation.