The groups (aka folders) of brushes are stored inside the .abr file.
You can test this by creating a group of brushes, exporting the group as an .abr and re-importing it.
Also if you click on the Option button in the Brushes Panel and choose Get More Brushes, then download the Kyle’s Brush Megapack you’ll see it is one .abr file. The folder structure is inside the abr file
I do see them in Preset Manager so I assume they are stored in the preferences, not actual folders.