Do you think her aides had the highest levels of security clearance? I doubt it. If they didn’t have the clearance, it would have been illegal for them to be the recipients or senders of top secret communications.
Probably yes. I worked in the State Department for 28 years. Those working on the 7th floor for SecState would almost surely have such clearances. They couldn't do their jobs without it. Huma and Mills held positions where they needed the clearances. Mills was Hillary's chief of staff.