If you would have create an page called "admin" without shorturl and with the pages removed you would be in more trouble..
"admin" is a system folder used by WB. A url like "www.yoursite.com/admin/
" should open the backend always. The website cannot decide if you want to look at a frontend page called admin or a backend page with the same name.
It is possible to change the /admin/ directory to something else by renaming the directory and creating the ADMIN_URL and ADMIN_PATH constants in the config.php (like in <= WB2.8.2), but the same problem for other system directories will always stay.
Using shorturl, the admin page is created as /pages/admin.php. With /pages removed it would have been written as /admin.php.
Creating a childpage in this admin.php would create a new /admin/ folder, overwriting the backend files.
Removing or renaming this would remove the backend completely.
That is the main reason to "NEVER" remove the /pages/ completely in the settings.
I am thinking, if I had just changed my pages directly to the root like I used to, I would not have had these problems.
If you did that, you would have had no backend at all anymore.