I read a very old topic about almost the same question which I have: would it be nice to modify this wonderful plugin in a way it stores the actual binary-files in subdirectories. There are many reasons for that and the filesystem-performance is one of biggest and most important (also backups, modifying/deletion etc.).

I took a look at the code, and I think it should not be that big update (except migrating the old installations): the method which gives the photo's full path could have {$albumId} before the filename (albumId was not sent to that method though...). And when uploading, that subdirectory named after the album-id should be created. Album-ID would be perfect, because photos seem to impossible to upload without an album.

Please let me know what you think,

Olli