JS and CSS image path
If I understand correct, no need to hardcode images: Add any image through the Drupal program itself via the API or background images via the css and a relative path:

For example, if your image is at theme/images, do {background: url(images/image.png);} or {background: url(../images/image.png);} if your css is situated in a folder of it's own inside the theme's folder.

You could filter or manipulate specific images with JS globally via a custom js file for your site as explained here.