What advantage is there in reporting the Lennard-Jones well depth in wavenumber units?
I don't think there's any inherent advantage as one can always convert to another unit. It seems natural to me, however, because chemists generally have a good idea of the energy of vibrational and rotatial states in $cm^{-1}$, so being able to compare the depth of the well with some familiar chemical process is quite nice. For instance, if the well-depth were quite small, one could immediately identify that the system may not spend a lot of time there if it is comparable to the zero-point energy or something similar.

It's similar to how physicists report everything in electron-volts ($eV$). They do it because it's familiar and they have many physical processes they can use as a reference. For instance physicists know that the band gap of semiconductors is between $2-5\ eV$, so it's quite natural to report other energies in the same unit.