I've ran into quite a few engineers from unrelated backgrounds that put unpopulated components on the BOM. Some will do a section clearly labelled DNP at the bottom, others will leave them dispersed throughout the BOM, but highlight the rows.
Having a DNP section seems like the way to go if you must do this, the only downside I can think of being that there will have to be more manual editing of the CAD package output. (Have personally witnessed this, the DNPs were changed at the last minute, the DNP section didn't get editted properly, and parts that shouldn't have been on the board were placed.) Leaving them throughout and highlighting the rows seems suboptimal because there could easily be duplicate rows for populated and not populated, and again, more manual editing.
I don't see why this practice is necessary. A BOM by definition is a list of things required to build something. If a component is not on the BOM and assembly drawing, it should not be on the board. Adding components that aren't actually there just seems like a source of confusion further down the line for whoever enters the BOM into the ERP and purchasing. What does putting unpopulated parts on the BOM achieve that leaving them off the BOM and assembly drawing doesn't?
Best Answer
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.