I have several multisites but just one using the New Blog Template plugin. On that site none of the templated sub domain sites are seen at all by the search engines.
Fo instance - Your search - "sitename.maindomain.com/" - did not match any documents.
This site has been manually submitted to Google search and is two weeks old.
The site I use as my "master" for the clones is searchable. (Though I have made it private and the others public)
What do I need to do to make these sites searchable. I have quite a few now.