Review how Atomic Search treats dead content, or content that is not linked anywhere in the course.
Does “dead content” appear in student search results?
If you do not enable the Pages menu for your course, pages that are not inserted into modules or linked to from other pages that are accessible will not be searchable by students.
Similarly, if you do not enable the Files menu for your course, files that are not inserted into modules or linked to from other pages or files that are accessible will not be searchable by students.