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?
Because WordPress is not scanning all the folders all the time. When you upload images Wordpress also makes an entry in the database, records the caption, the sizes that are available and so on.
There is a plugin Add From Server that allows you to select files from the "uploads" folder and import them in the Media Library.