I wonder if polygraphs are there as a cover for refusing clearance due to secret evidence. If you know bob is a Soviet spy because your agents in Russia say so, you don't want to blow their cover, so you need an arbitrary reason to refuse clearance.
"Of course, the whole point of a Doomsday Machine is lost, if you keep it a secret! Why didn't you tell the world, Eh?"
Benway's panopticon only functions if the inmates think they are watched. The secret might be that they cannot actually process all the data and are overwhelmed by the sheer quantity of it, in which case the surveillance is more useful if people think they can.
Parent is getting at the fact that it is entirely possible to have a Top Secret clearance and never be granted access to any interesting information.