The structure that you are seeing is correct for your projects. HP defines the smart repository storage system in the following way:
''ALM stores all project files in a project repository located under the ProjRep directory. The files in this directory are stored in an optimized folder structure that allows maximum storage space. In addition, any two files with identical content are stored only once in the ProjRep directory. This results in a significant reduction in disk space. For example, if you attach the same file to several ALM records, the file is stored only once in the project repository. Periodically, ALM clears the repository of duplicate files.''
If you would like to view the file structure in the older/ traditional way that QC used prior to ALM 11l, then you would need to FTP into the ALM/QC 11 file server (this can be accomplished by adding the following parameter to the site configuration: ''FTP_PORT and then the value of the port number, generally 21 is used, and then connecting to the server through an FTP software, such as filezilla, to see the traditional file structure hierarchy.
I hope this helps,