IMHO, I bank on “Crooked” not wanting any more light shed on her activities during the past six years as reason why she gave up her security clearance. Having officials during this administration actually doing their work is just too big of a gamble.
Elected federal officials don’t have to pass security background investigations. But appointees do, up to and including the secretary of state.
And to keep their clearance eligibility, they have to undergo periodic reinvestigations, just as mid- and lower-level officials in the federal services do.
The timing of the access withdrawal is interesting. Although the Pentagon extended the interval for a periodic reinvestigation from five to six years in 2017 (for Top Secret access), the State Department’s website still says the interval for its personnel is five years. Based on when Hillary Clinton and her aides were in their jobs (2009-2013, with the first background investigation forms submitted by them probably at the end of 2008), the completion of their next periodic reinvestigations is probably due in early 2019.
That would mean they’d be submitting the paperwork right now for their reinvestigations. It’s possible Hillary Clinton didn’t want a new background investigation done on her or her top aides, and elected to have their access withdrawn instead.
We have no way of knowing if she was encouraged to such a decision by any quiet consultations with contacts at Foggy Bottom. But as a veteran of the investigation process, she would know the questions she’d be asked, and the kind of information investigators look through. It’s possible she didn’t want to turn that klieg light on. The last time she and her aides would have done this, in 2013-2014, Obama was in office.
Partisans would read that in different ways, either as Hillary having things to hide, or as a fear that investigators in Trump’s administration wouldn’t be fair with her. You choose your perspective. This seems, however, like a not-improbable reason for doing something peculiar like asking out of the blue to have your security access withdrawn.