What standards or conventions are there for BOM line items for non-refdes parts?
The best way to handle parts that don't appear on the schematic is to fix the schematic so that they appear.  If you don't, you'll constantly be manually fixing the BOM that is automatically generated by your tools.

This applies to all the parts that belong to the immediate built board assembly.  At the least, these are the parts that get soldered or otherwise mounted to the board.  If the built board is part of a larger assembly, then the BOM for that assembly will show the built board as a single line item, and it can call out screws, nuts, standoffs, etc, for mounting the board into the larger unit.

And yes, this applies to sockets too.  For example, here is a snippet of a larger schematic for a real commercial product that exists in the company's formal manufacturing database:



P11 is a Phoenix Contact connector that accepts a plug with screw terminals.  Only P11 actually gets mounted to the board, but there always needs to be a plug with the board.  That's what PLG2 is.  It is there primarily for the purpose of automatically appearing on the BOM.  In this case I think showing it on the schematic is also a nice visual reminder that the board comes with a screw-terminal plug.