filesystem search and access is different when you're talking a single larger file versus multiple smaller files. All filesystems have a per-file overhead that would effectively be eliminated if you could pack all of your files into a database structure. Indices would also speed up access to individual rows of the table significantly.

There is overhead in small file storage anyway, if the files are not the exact size, or a multiple, of the sector size. storing 1kb files on a disk where the sector size is 16kb is far more of an overhead expense than storing those files in an SQL database.