When replicating a website all the template are automatically defined.
I suppose that the symbolic Link are OK and the "replicMasterSubdomain" rule should have created a link on the "/templates" directory.
So all the templates should be there.
Some template companies like "YooThemes" requires an additional "Patches for Yoothemes" extension.
www.jms2win.com/en/joomla-multisite?page...46&category_id=1
So if you have a problem of display on Yoothemes template, you need ot install the patches.
If the Yothemes template is not in the list of patches, you can send us the template for review to the "contact us" email address.
www.jms2win.com/en/contact-us