A friend of mine has the same experience. They answered yes to the marijuana question and still got clearance.
Another friend lied and said no (this was for a college internship so I knew a couple people working there) and got rejected once their story didn't check out with their personal references.
The interview/form is looking for potential blackmail or tendency to lie or obscure facts. If you are honest, that's fine, although they sometimes ask that you are currently using as well and that is a strike against you.
I was talking to an NSA recruiter last year, though, and they told me they routinely report applicants to the FBI for confessing to crimes during a polygraph. So damned if you do, damned if you don’t…
(For a recruiter he did an uncanny job at convincing me never to work for the NSA)
I mean, that might be true if someone confesses to heinous/violent crimes (and shouldn't they?) but its definitely not true for things like minor drug use/sale etc.
But if the crimes that you confess to are skilled hacking crimes and the NSA hires you anyways, then the FBI never finds out ? Thus making the NSA judge & jury.
Another friend lied and said no (this was for a college internship so I knew a couple people working there) and got rejected once their story didn't check out with their personal references.