The concept of JMS is to share the same joomla application (php code, installation).
The dynamic content of the website is generally in the DB and each website have their own content.
Therefore if you want to create website with specific joomla /templates directory and have specific DBs for each websites the you will not share any content.
That mean that the menu, articles, ...., will NOT be shared.
So if you create a new menu item in one website this will NOT affect the other websites as each website have their own DB and own content.
To simulate partially the menu sharing, you have the "Multisites Menu Item" that allow creating a link between the menu item of 2 websites. So that when you modify the definition of the menu item, the other site is reflected by this menu item modification.
Concerning the symbolic link, this is the same as a shortcut on windows or an alias on macintosh. This allow create a link between a physical directory or file without duplicating it.
You can not create a link on yourself but you can create a link to a parent directory and therefore create an infinite loop. JMS may create such kind of link depending on where you deploy a slave site. When it is deployed in a subdirectory of the master, such loop can exists.
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