Uploading directly to the wp-content/uploads folder using FTP or likewise will not make it show up in the Media Library. The files have been uploaded successfully, but WordPress requires the media ID to be added to the database. Only once the media ID is added to the WP database do the files show up in the Media Library. Uploading an image through the Media Library on your dashboard does this automatically, but there are situations (like in your case) where you may need to upload through FTP or some other direct file management means.
You can use a plugin such as Add From Server to add the media ID to the database for you.
Note: this plugin hasn’t been tested with the latest few versions of WordPress, so use at your own discretion. I’ve used it many times in recent months without issue, and I just tested it with the latest build of WordPress and it also worked without issue.