Er, the point about the 1,000+ files in a single directory, while uploading multiple files to this same directory is this:
Most FTP clients will request another dir listing after *every* upload. When you're uploading things like small pictures, the dir listing may indeed take longer than the actual upload. It could concievably take forever if you had a large enough list of files to upload.
So yes, of course it does not control throughput whatsover, but it may very well indeed effect "total upload time" or whatever you deem fit to call it.
-Phil