I upload thousands of images and it stored in a single folder. Is it bad if too many images are in a single folder? would that slow down the loading of the image even though you're viewing an attachment image which has a path defined?
No the depth of your directory structure has almost no impact to load time.
Maybe if your structure is very depth and the URLs for the images are very long you can hit the maximum length or your markup blows up. But a flat hierarchy should not be a problem as long as you keep the file names short enough.
Then again, if your store everything in one directory, there may be name collisions. But WordPress checks for that during the upload with