Users will be getting a digest because they will have selected the option to follow a folder (That is the yellow star next to a folder), and have their mail option in their profile set to digest.    If they unfollow the folder the notifications should stop.  With follow enabled the user will get notifications (either digest or individual mail) of any changes to the file or folder.  At a guess it looks like users will still be accessing the folder system directly, (not through filr) so any changes they have done will be picked up by the sync.

I would not disable your scheduled synchronization, especially if you do not have JITS enabled. Typically I would have it once a day, if it is taking a long time to complete then maybe once a week, or consider a dedicated synchronisation node.

If you are not sharing files then you can also disable all mail on the email tab in the Administration Console.

Thank you. Is there a way to look at the DB to determine who is following a folder? What tables would I look at?

Look at this  Show subscribed items  ... and vote.

However I assume that ss_subscriptions will tell us the truth ...

Thank you.

In ss_subscriptions, what does the entityid refer to? Entries in ss_folderentries?