I also have this issue, and I was wondering if any functionality has been added since this answer was posted back in 2015.
To be more specific about my question: Is there any way for a CA Agile administrator to generate a single list of all custom reports that have been created in all projects in a given workspace, without having to traverse the entire project tree manually?
I have posted a proposed fix for this on the CA Agile Central Ideas board:
If you are experiencing this or a similar problem, I encourage you to vote for this idea. Thanks!