How to deal with unused components in pick-and-place file?
Personally I'd do the opposite of @CrossRoads, leave the reference designators in the BOM. If you set the value to DNI or DNP (or NM) with no other part numbers, all assembly houses will interpret this as meaning do not place.

If you want you can also add a column to your BOM which by true/false entry indicates whether a part is populated, however DNI/DNP should be enough.

The reason I'd suggest leaving the ref des in the BOM is that most assembly houses will examine your data and try to match up BOM entries to the silkscreen (even if you provide coordinate data). If they find parts on the silk that don't exist in the BOM, they may query you as to what should be done with those parts. If you mark them as unpopulated in the BOM, they have all the information they need without having to query it.