"To add CSS or JS that should be present on all pages, modules should not implement this hook, but declare these files in their .info file."
CSS files can be added to a .info file using the following format:
Images, JavaScript, and Flash files that PHP sends to the browser are not affected by the GPL because they are data. However, Drupal's JavaScript, including the copy of jQuery that is included with Drupal, is itself under the GPL as well, so any Javascript that interacts with Drupal's JavaScript in the browser must also be under the GPL or a GPL compatible license.