We're talking about renaming folders, not files - hardlinking only applies to files, the rough equivalent for folders is junctions.
FAT32 aside - I cant see why one would not prefer to enter the new name once - into calibre, rather than twice - once into the file manager and then into calibre. Just as one does for author and book folders; if one trusts calibre to get those right (which is complex because of the need to change the format file names) then why wouldn't one be happy letting the calibre take care of library names - which are by comparison, trivial
BR