When adding a bible passage to clippings Logos 4 add the bible reference (bottom left). But when adding a passage from NA27 there is no reference added.
If adding a clipp from BHS Logos add the reference.
This doesn't work in 4.0 either. It must be a bug that was never reported in the current release version. I checked and references do appear using the BHS w/Westminster 4.2 morphology.
I'll submit your report to development. Thank you.