We've logged your bug, and it should be fixed in upcoming versions of clearspace. You can track the progress of the bug here: http://www.jivesoftware.com/issues/browse/CS-1676
In the meantime, if you need to get rid of the empty sub-community tab you can add some <#if> statements to community.ftl, doc-macros.ftl and forum-macros.ftl.
In each of these files there will be a block of code labeled with the comment <!-- BEGIN communities list
> (and <!BEGIN communities list (hidden)--> for the bit that hides it.) You can just surround these with a test to make sure community.communityCount is greater than 0.