How do I disable digest subscription notices for all users? I expect to do this in the database rather than through the UI. I thought I'd done it already, but it seems they are still going out. Any help would be much appreciated.
I'm not sure you'll really be able to force everyone out of getting Digests, but if you look in

/admin/config/system/subscriptions/userdefaults

In the Settings Fieldset, above Type of links to send field, there's a checkbox for Digest mode. If that's checked, it may be causing you problems.
I'm looking at this in D7. 

My main thought is that user preferences for a digest may override the defaults you've set up, so I'm not sure you'll really be able to completely shut down this feature. I'm also not sure why you'd want to. Getting pinged about a new comment every time it happens can overwhelm someone's inbox if even a moderate conversation is going on. My team likes giving a digest every 3 hours as the default because it will give users about 2 updates a day, but won't overwhelm them unless they change the settings themselves.