What to do with hidden files in Drupal 8 minor core upgrade?
TL:DR;
You should delete all files hidden and not hidden that you didn't place there yourself.

Drupal core has a lot of hidden files, which are used when developing Drupal itself (git, lint and possibly more) but none of those are needed or relevant for running a Drupal site in production. They are highly relevant when you are working on Drupal itself.

The only hidden file you need for a production site is the .htaccess, if you have more than that they are safe to delete.