I (finally) found the source of this bug. The author archive redirecting to the homepage is saved in the options under the key 'disable-author'. The problem for me was that this key was in two different options records: wpseo & wpseo_titles. This is most likely due to the author changing the location where this setting is saved at some point, but the upgrade process didn't clear the old record.
To fix this:
1. In the WordPress admin go to SEO -> Titles & Meta, click the Other tab & ensure Disable The Author Archives is unchecked.
2. Go to your database and find the options table for your site (wp_options or wp_XX_options most likely)
3. Find both rows with option_name set to wpseo and wpseo_titles
4. If the key "disable-author" is set in either of them you can remove it entirely, or change the value of it to "off"
If it is on, the option_value for either/or both of those rows will include: s:14:"disable-author";s:2:"on"; That's the part you can remove.