I have a simple rom structure: roms/platform/xxx.rom and also rom hacks stored like this: roms/platform/hacks/base_game/hack.rom.
When building up my initial library I dragged and dropped the root platform rom folder for each platform, and all roms were found. I enabled automatic import as well. Later added some roms to one of the root platform folders and also to another platform's hacks folders. Automatic import found the new roms in the platform folder, but not the ones in the hacks folders. Doing a manual scan for new roms also did not pick them up.
For automatic import there's no way to select sub-folders on/off, and when scanning for new roms manually I made sure to allow it to look into sub-folders.
In the end to import those roms I had to drag and drop them.
