-Financial debt, so all of your finances are inspected
-Family connections, so all of your family is investigated
-Marital affairs, so you're asked about it during the poly
-Pirating software, again asked about it on the poly
...and all sorts of other things. The big thing you hit on is that this isn't very painful unless you try to hide it. If you try to hide something and it comes out in the investigation, you'll almost certainly be disqualified.
Also, polygraphs are pseudoscientific nonsense.
The NSA, at least, is not without imagination. They will have perceived the issue with making a stink about X causes X to be a handle for coercion. Therefore, the NSA wants pot smoking to be in issue they can disqualify people with, they want other arbitrary categories of actions to be disqualification issues. Why? My guess is control: mental health issues and sexual behavior outside of vanilla are pretty darn common. Finding such problems gives the NSA itself a handle on their own people, to coerce things from them.
And as far as "character" goes, haven't we heard enough about that in the past few years to realize that "good character" is just another form of racism/elitism, like "good breeding" or a "gentleman's C" grade at an Ivy League school?
If instead they just decided that if they found out one of their employees smoked pot that they wouldn't care the coercion potential would magically disappear overnight.
But I guess that's too logical for the government to consider.