Maybe I should have clarified what I mean with "huge", obviously a few thousand is not huge. I am more thinking about millions of small files. Normally OS's don't like directories with so many files. (The OP doesn't have millions of files though.) It's nice that some OS's have better support for this nowadays but the OP didn't specify his OS/version, maybe he is using and old Unix/Windows OS? Chopping things up in subdirectories will also improve search/access times.