I've gone for editing the vmx file to specify following symbolic links (which does work for Windows VMs) — thanks for the suggestion.
I mentioned my use of a folder comparison tool. I use that for making short-term backups. In order to avoid making duplicate copies of the directories that are linked to, I've set up a filter in the folder comparison tool.
EDIT:
So, my filter in the folder comparison tool lets me see that I've added a symbolic link, but when I copy things across subfolders are not copied.