Fewer Application Groups with more Applications are better. Each Application Group you 'bind together' at the Folder level is a separate query -- why do 25 queries when you can do just one?. If it supports your needs, one AG with 200 Apps is the way to go. You can use the AppID field to filter/restrict your results at query time.
If your volume is high, increase the max rows per table to equal your approximate monthly volume, plus a multiple of your expected annual growth. (So, 55 million documents a month with 10% annual growth = 60 to 70 million rows per database table.) This will help keep performance linear as your system grows.
-JD.