Organize in such a way that maintaining it is easiest. Have as many subdirectories as necessary to keep it organized and meaningful. For small sites I only have a single directory for images. For larger sites I'll have subdirectories for specialized images (icons, buttons, photos, temporary, etc). That makes it much easier for me, and anyone else who has to maintain the site, to figure out what the heck is going on when we revisit the site months or years later. And with images, and similar files, your users never see the URLs of those files so they can be longer and won't inconvenience them one bit.
The only issues you may have with many subdirectories is when it comes to web pages. If you have too many subdirectories it will result in longer URLs which can be inconvenient for users at times. Then again, sometimes this will be a natural byproduct of a site's content. In these cases plan ahead and try your best to find a balance between maintainability and usability.