The $25 billion in black budget funds we spent developing the airplane is what killed it. When the amount became public, Mr. and Mrs. America got sticker shock.
It makes a case against black-budget funding: better to see how much it's costing while it's being developed.
I would think the end of the cold war and the associated heavy handed evisceration of the defense budget had alot more to do with the death of the B-2 program than public outcry over the secrecy of it.
I also don't really have a problem with black budgets for defense. A little knowledge is worse than none as far as stirring up wrongheaded outrage, and the tactical aspects of national defense are too important to be left to opinion polls. From an academic standpoint I'd like to know where my money is going, but not if that knowledge will be abused to impede the military from doing their job.