For performance reasons, it's best to create Application Groups with multiple Applications, rather than binding a variety of AGs together at the folder level. This is especially true if one or more of the AGs has tens of millions of rows. If it makes sense, consider consolidating your AGs.
If a new consolidated AG doesn't work in your scenario, keep the number of mapped AGs to a minimum, and increase the number of rows per database table for large AGs (ie, more than 10 million documents per month).
Also, turning off 'Display Document Location' if it's enabled will help maintain performance.
-JD.