It's got to be pretty intimidating. Getting locked up in a room with the investigator, being told that you're not actually required to be there, but it will seriously jeopardize your chances of employment if you decide to leave or decline, etc. I'm sure it works well as an intimidation tactic, as you say.

People need jobs and are willing to put up with lots. Going through with a polygraph is likely just one of a number of the things that people in these industries have to put up with.

It is extremely intimidating. My interviewer decided that he was going to tear me apart and that he knew I was lying about something (I wasn't). He said he could only help me out if I admitted I was hiding something and told him why. I stuck to my guns, told him that I wasn't hiding anything, that I was sorry that it seemed like I was, and that I would be able to sleep soundly knowing I had been honest on my test, even if it appeared otherwise. He didn't like that a whole lot, but I told him I'd rather fail the process having told the truth than pass it having lied on it. Ended up leaving that job shortly after largely because I didn't want to do the polygraph. Fuck that noise.

I'd imagine it's also a good way to filter out non-sociopaths from the three letter agencies.

For the NSA/CIA, I imagine there is still doubt, even if you've looked it up. "Does the NSA know something everyone else doesn't [about lie detecting]?" is not an easy question to answer.