It's much more likely that this stuff is difficult to do, and thus difficult to price out, than that somehow the managers of these companies are working with the finance people to secretly steal money from the government and hide it in their books, the government never catches it, and these very amicable ties between the government and defense contractors continues - and all of that is before we even get to what happens when you try to steal and your project falls
behind.
It's way more valuable, usually, to get it done quickly and done well the first time, so you can move onto another project. You leave a few people on the original program pull in tons of super easy maintenance contract money for what essentially ends up being a skeleton crew.
Or, I suppose, you could try and inflate costs by a couple percentage points (not too much - you'll get caught and the risk here is MASSIVE), keep working on the same program, and hope the opportunity cost doesn't get too high.
I'm sure it happens, but I doubt it happens often.