When someone registers (creates an user account), entries are automatically created in the [prefix]_user_notifications table (most commonly phpbb_user_notifications table).
Depending on preferences in the UCP, other entries can be created for a given user.
However, if an admin deletes or prunes user(s), no entry is erased at all in this table.
I experienced this on a board where I have to prune thousands accounts. More than 100,000 rows of unused entries are still present in the database after the deleting (roughly useless 9MB in SQL file, on a whole database of 70MB in SQL file). If I delete some accounts individually, the problem is the same. Therefore, it's not just a prune-related problem (the prune process is also a mess since deleting more than few hundreds accounts at once generated a timeout for me but it's another and know issue).
A proper user deletion should remove unused entries, just like a proper uninstaller should remove unused files and entries in the Windows regedit.