[itronitron]

The main point of the screening is to have a highly structured question and answer session that is recorded for posterity, and which can/will be referenced at the next screening 'n' number of years later.

One could even argue that the polygraph benefits the person being screened, as it provides some additional motivation for them to take it seriously.

[themafia]

The FBI and CIA have polygraphs.

The FBI and CIA still have moles and they often times operate out of the highest levels.

They're like door locks. They keep honest people honest. They provide zero security.

[varenc]

Door locks are a deterrent that increase the difficulty and cost of a crime. If your neighbor's house is locked and yours isn't, then you're going to be more of a target. In that sense they do provide security, but of course any lock might still be defeated.

Similarly, I can see how structured psychological interrogation, assisted by a polygraph, is a useful deterrent. The presence of moles doesn't negate all of its value. Just like having your house broken into once doesn't mean you'll stop using door locks.