I think you may find that the index.php file you refer to is there by design. If your server allows browsing by directory and you don’t specify Options –Indexes in your .htaccess file, anyone can view the contents of your folders simply by requesting them in a browser. That file with “//Silence is Golden” in it, returns a blank page if someone were to intentionally request "yourdomain.com\wp-content\". I think it is intended as a deterrent for anyone who might be poking about trying to see your wp-content folder.
Download a fresh copy and unzip it to verify that it is there by intent. It will put your mind at ease.
As far as the folder that creates itself, and that you can not delete, You may want to ftp to your server, check the owner and permissions on the folder(s) and files, and investigate from there. If it becomes clear that it is not the result of something you may have introduced to your installation through a plugin or a file from a unknown source, contact your host and see what assistance or info they might be able to provide.
A Google search of your folder naming convention (DWddXX123), turns up some interesting results;
See: Index of /~u92125271 , if you are the investigative type.
You could also Google the known program file extensions for .DDD and see if it rings a bell with any apps you may be using. (Acrobat Distiller, Bullseye Style Sheet...etc).
Good luck to you.