If they filter out some classes of security threat by other means is not so clear.
That is a claim that has ZERO evidence and zero reason to suspect anything other than tricking people into thinking it works. You might as well claim that polygraphs give you mental superpowers. There's just as much evidence to support it.
In regards to real world applications with some degree of actual evidence, the only thing that polygraphs could be useful for is tricking people into thinking they work. But you could substitute countless other techniques from different cultures and claim mystical powers. But if they literally used a voodoo ritual as part of getting a security clearance, people would obviously get upset because that's clearly stupid bullshit that would only let crazy jackasses in.
Just because there are experts who are idiots, doesn't mean that any experts is non-expert, or an idiot, or can't be trusted to manage their own damn employees. How would a non-expert such as yourself hope to impeach their judgement? You can't, of course. As you point out, their field is shrouded in secrecy; that means you don't know, it doesn't mean they don't know. It means you can't judge what they do effectively. Now, there are lots of legitimate policy opinion responses to that situation. But it doesn't leave you in a position to impeach their judgement about things where the facts are mostly secret.
Secrecy is not an advantage in regards to having scientific evidence. It means that they aren't subject to external peer review, and thus have little to no forces that act against their existing biases.
And they're not bumbling morons, regardless of your or my opinion of their polices.
According to spies themselves, they often are.
The whole organisation was riddled with nepotism - dim, dreary people of utter unmemorability; sub-men who were doubled up with other sub-men to create an illusion of strength and only doubled the weakness; others made memorable only by poisonous, corrupt malevolence or crass, mulish stupidity; the whole run by a chain of command remarkable for its feebleness. The entire service was decrepit and incompetent.
How come everyone's going so slow if it's called rush hour?