Why put unpopulated components on a BOM?
If you don't explicitly document that these components are not to be placed, you will inevitably have your manufacturing team notice that there is a location on the board with no corresponding line in the BOM, and delay the build to send an engineering query asking what is supposed to be placed there.

Explicitly documenting not-placed components avoids these queries, much like "this page intentionally left blank" in the manual avoids people asking what was supposed to be printed on the pages that were blank in their copy.