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I'm fairly "outdated"/not very knowledgeable about really having and up keeping a lot of images, but I do have around 40,000 images in my "anime" folder.
First, I have them organized into separate purpose-based folders such as "cute", "reaction", etc. Then I have different sub folders for specific characters, or if the image focused less on the character and maybe an action or detail like "crying" or being pet or "neko" or something, then they get also get put into folders. If you don't let it all pile up, it's not bad, and very handy. I just sort them as I get them and it's no biggy.