An update, because I think I found the issue.
I downloaded the CSV file of users and noticed that a lot of people who had email notifications set to “on” had only the most recently created categories checked.
Then I went back to the settings and found that users were automatically subscribed to new categories.
This switched their notifications to receive daily digests back on every time I created a new category. People who joined recently (after the last category was created) do not receive email at all.
I’ve now switched off the automatic-subscription-with-new-category setting, but since we’re not planning to add more categories, it’s hard to check if it works!