Well, as Gerardo mentioned, what if you get 50k users? (it happens) You'd have to create a storage routine that creates subdirectories etc. very messy.
"and DO NOT need to search through the config variables"
that is the point, such files are very rare.
And where they do exist they complement dynamic data from a database, in which case it is better to just put everything in the database and save the extra hit on the filesystem.
Speed is important, but not paramount.
Imagine if your system has 10k users, and you want to change one particular setting for each user. Do you really plan to change 10k files?
And what if your system crashes while it is re-writing the config file? Databases are prepared for that, the filesystem is not.
Flatfiles are very fast (which is why sessions use them by default) but they are also rapidly becoming redundant.
In a good database setup, a database call may even be faster than the filesystem providing the query is simple enough.
But the main point is maintainability. There is no way on this earth that you can make a flatfile system as easy to maintain as a database. You'll end up writing pages and pages of code just to be able to work with the flatfiles, and what you end up with will look like... a database. 🙂