Have you considered making the symlinks relative instead of absolute? I just went through the process of migrating a site from a dev environment to a qa environment (same server, different path) and I had to write a script to go through all the symlinks and change them from pointing to the dev directory structure to the qa. If the symlinks were relative this wouldn't have been required. It would also make it easier to move from one hosting provider to another (or to move from localhost to a live host).

The path is the one that is provided in the slave site definition.
When you are using a JMS Template, you can use keywords that will be resolved when the website is created.

All depends on the way that you move the environement.
If you are doing in backup/restore with a linux command like (tar), perhaps you could ignore to backup the link and rebuild them when you open/re-save the slave site with new deploy directory (or empty the field if it is compute with a JMS templates rule).