It was about two years ago that I noticed there was a minor issue with how wp_get_shortlink handled things with the default permalink structure. This is what I wrote in my original ticket:
Currently the code used in the link-template.php file causes the wp_get_shortcode function to return an empty result if the WordPress installation is using the default permalink structure. This causes at least issues with the_shortcode function and can be expected to cause issues any place that wp_get_shortcode is called when the default permalink structure is being used.
Obviously this was not a pressing issue but it was fixed on the 25030 Changeset. Props went out to sillybean, layotte, and cais (me!).