Can't answer your question, but I just had a poke around with Query Monitor and this is the query that seems to get all the categories (it runs last so you don't have to search through every single query). If you can be bothered running this against your database and having a poke around with the results might help you figure out what's going on.
Or maybe you want to use Query Monitor to double check what query gets run for you to see why not all the categories are returned.
SELECT t.*, tt.*
FROM wp_terms AS t
INNER JOIN wp_term_taxonomy AS tt
ON t.term_id = tt.term_id
WHERE tt.taxonomy IN ('category')
ORDER BY t.name ASC
Edit: And if this query shows all your categories, then you know that something else is removing them from this view somehow.