Please see this thread which outlines the conditions required for the system level and course category level question banks to be included in a course backup: https://moodle.org/mod/forum/discuss.php?d=377855.
If quizzes are dependent upon questions in the system or course category question bank those need to be included in the course backup if the course is going to be restored to another instance of Moodle. However, there are some internal operations such as Import and Upload Courses (using a template) where the course backup is guaranteed to be restored back into the same Moodle environment. As such, if a course backup is being created as part of an Import (or other "internal" operation) there is no need to back up the system question bank as the restored course will still have access to the same system question bank. Likewise, if it can be determined in advance that the Import will be restoring the content into a course located in the same course category as the source course, there is no need for the course category question bank to be included in the backup.