That's fine for file storage, but doesn't provide a way to find all photos with dog in them, or photos from 2007 - 2012 with bird and dog, but not cat, in them.
Most apps will let you store your photos how you want them to be stored on the filesystem.
It doesn't seem like a good idea to tie a photo library to any app. Applications come and go, the photo library should last a lifetime (or more if you pass it on). You don't ever want to get caught with your photo data in some proprietary structure when the app that created it is no longer available for whatever reason. My photo library certainly has outlived many applications I've used to process the photos.
After processing I store them in just a directory hierarchy. Top level dirs for each year, event/topic subdirectories under each year. That's it.