Best practice for wire harnesses in a BOM
It's typically best if the BOM reflects the assembly process. Start with the final product (or whatever goes in the box to be shipped) and work backwards through the subassembly.
If the harness gets build on the final line, than only the parts (wire, crimps, etc.) should be in your BOM. If it shows up on the line pre-assembled, than it's a subassembly with it's own part number and sub-assembly BOM.
Most BOM management tools allow you to structure the BOM this way and also create a &quot;flat&quot; view, where all parts are listed.