Enable CSS files in Omega 3 sub theme with Drush?
I'm only a bit familiar with Omega 4. In order for your css files to be "enabled" by default, you need to transfer the theme settings from the database into the theme's .info file and make sure this is enabled also in the live site. So if you have css/style.css and its declared in the .info file, Omega 4 will just follow the .info file.

Hope this helped. :)