That's sometimes true but it depends a lot on the filesystem used, and sometimes on the options used when building it. ReiserFS, ext4 and FAT 32 won't have the same performance profile.
I think breaking down large collections in subdirectories is mainly done in order to ensure that it'll work even with FS that don't deal well with very large directories and also because it makes inspecting the files manually a little more convenient given that many file explorers (and especially the GUI ones) can have trouble with large directories.
I think breaking down large collections in subdirectories is mainly done in order to ensure that it'll work even with FS that don't deal well with very large directories and also because it makes inspecting the files manually a little more convenient given that many file explorers (and especially the GUI ones) can have trouble with large directories.