Using subdirectory trees fixes an ancient UNIX problem that happens when there are several hundred of files in one directory -- if this is allowed to happen the system will sllloooooowwwww ddooooooowwwwwnnnn every time the full directory is accessed.
yo! don't generalize! my ReiserFS deals quite fine with tens of thousands of files in a directories, and probably more :-)
Yo! Hence my use of the word "ancient".
This problem still exists in ext2fs and ext2fs is still the default filesystem on most Linux distributions. The mediawiki folk are smart enough not to force everyone to use reiserfs should they not want to. ;-)
Brian