Filesystem is essentially a "simple" database. If it is not performing, then it is not a good db. It shouldn't really matter how many files you have if metadata, and indexing of that metadata is done properly (i.e. like in good db). It also has additional benefits to DB that usually do not even exist there as they aren't practical at all (like random access).
The problem with file systems is that even if it's a competently implemented DB, it's a DB where you cant (easily) change the schema, put type restrictions on the columns, or customize the indexing. File systems are great, but if you have a lot of data, using the right tool for the job is a lot better.