You probably fixed it already. Just in case though.
You could use powershell to automate creation of sub folders and moving files into them.
I would not though.
5000 files isn't that many. It's not sheer number of files. NTFS can handle hundreds of thousands of files.
If you have no shell extensions on windows explorer then it is almost certainly your thumbnails.
Disable that entirely.
Stick to explorer list view and text only.
I definitely would not use the bonus tip advice in that link and install a PC maintenance tool.
I agree with Kurgen in that it sounds like you've got very big hi res pictures when you need smaller lower res for ebay.
Maybe there's another reason you want hi res pics but I'd suggest keep those big ones on an external drive.
Or 2
Always 2 copies of anything you really care about.
Preferably 3.
I dunno about ebay and external links.
Could you use linked files there?
If so I'd also consider putting the pictures on imgur or some such.
You get another back up for free.
I like imgur: