Why does file_create_url() not work for theme images? With the latest Drupal 6 update, file_create_url() stopped working for all the files other than public or private files.

I think the assumption is that a file must be either in the public files or in the private files directory.

How can I get the image URL for those images that are in a theme or a module directory?
You don't need file_create_url() to turn those URIs into a URL to use in theme_image(). 

For theming images in Drupal 6, just supply a path string relative to base_path() (the base of the Drupal install directory). For module/themes this can path can be retrieved with drupal_get_path(). 

For example:

//Render an image under the admin_menu project
print theme('image', drupal_get_path('module','admin_menu').'images/bkg_tab.png'))