have found similar issue :  http://www.telerik.com/support/pits.aspx#/details/Issue=5296
which look like has been fixed, but unfortunately for following case it doesn't:
We still have performance issue, in following situations:
   - when content root folder contains few (1-5) subfolders
   - one of subfolder contains lot of (200-500) sub-subfolders 

then first time RadFileExplorer  loading to long (aproximatelly 3-5min). after some researching has been found that problem in the method:  

     private bool HasSubFolders(string virtualPath);

which instead of simply check that folder isn't empty (exist any one file or directory)  always construct complete version of the subtree (in the example above - subtree contains 200-500 subfolders, each of them checking for content, permission etc - that is why it takes time). Probable to check that node  HasSubFolders, RadFileExplorer  could execute new virtual method of the FileSystemContentProvider bool HasSubFolders. In that case: FileSystemContentProvider (or inherited classes) will decide that Folder contains SubFolders.