Did you find a suitable solution for your folder structure? This is the best resource I know of in the Tableau domain for this question:
Of course others with ideas may want to add their thoughts here too.
I would recommend setting up your confidential data on a separate ”site” that will firewall it from the other data. Only the Server Adminstors can create sites FYI.
You may also consider doing this for your other folders as well. For example one site for your dashboards shared across the org and other sites for each dept. The benefit of this is you don’t want lets say the HR folder, or finance folder on the same site that’s shared across the organization. Best to silo those off from the others.
Here is an article that goes into more detail on sites.