This is a data point.
I have Skyrim SE and Fallout 4 on an SSD J:. I have a second SSD K: temporarily as a backup.
Using the command "robocopy j: k: /MIR", the K drive winds up with 369 GB used. J: has 331 GB used.
If I issue Purge from any of my Skyrim SE and Fallout 4 Profiles first, source and destination SSDs both show 331 GB used after the copy.
Points to note:
1) Deep copies will burn you. It replaces the hard links with the actual mods.
2) Purge before doing backups. In this case it saved 38 GB in the destination.
3) Most important - Purge before moving your game to a new drive. Trying to use Vortex on a new game drive where copy has "installed" all your mods is not likely to go well.
4) I have not found any Robocopy parameter that tells it to ignore hard links. I think I tried them all.