Always have a root site collection!!!
So today I spend most part of the day troubleshooting an issue with catalogs and host named site collections (HNSC) in SharePoint 2013.
I created a basic cross site publishing scenario where I had a path based authoring site http://intranet.contoso.com/sites/authoring and a HNSC publishing site http://www.publishing.com
All was going smooth, untill I wanted to consume the catalog. The catalog connection was found, but the navigation term set was for some reason not reachable from the HNSC. The error was thrown:
"We could not find the navigation term set for this site. Navigation integration and friendly URLs will not be configured"
I dove into ULSViewer, but there was nothing whatsoever in the logs that would indicate an issue. The term set was even reachable using the Term Store manager from the HNSC.
During the troubleshooting I noticed the root site collection did not exist, so I created one, but did not give much notice to it, until I was remembered by a fellow MCM that not having a root site collection could be an issue.
So I created a new HNSC and it just worked for that site. All other older HSNCs still did not work. The only way to get them to work was to delete the site collection and recreate it.
I have no details as to what exactly is the reason (there is an article specific to SharePoint 2010 http://support.microsoft.com/kb/2590564 ), but just remember:
Children beware! Always have a root site collection!
(this does not only apply to this issue; there are many other reasons why you would need it!)