What is the reason/s that the WordPress Media Folder, doesn't display images that were uploaded via FTP, directly to the uploads folder? Why doesn't WordPress "see" them? why do we always have to upload via the WordPress media uploader? What does it do?
There is a plugin Add From Server that allows you to select files from the "uploads" folder and import them in the Media Library.
When you upload a file using the default WordPress media uploader, it saves the file information inside the database. So, when you see them in Media, it means they exist and are registered in the database.
When you use other method to upload the image, like FTP, the database isn't automatically populated and, therefore, WordPress won't recognize their existence.