Let's assume that twentythirteen/shortcodes/ exists and inside are folders with shortcodes. 1 folder = 1 shortcode. Each shortcode has: 1 PHP file, 1 CSS file, 1 JS file.
twentythirteen/shortcodes/load.php exists that does
wp_enqueue_script() for each JS and CSS file. Furthermore, it has an option to generate twentythirteen/shortcodes/style-cache.css and enqueue only this one (or all JS and CSS files individually).
The structure described above makes it very neat and modular but this will not work with Child Themes? Is there any way to make it work like that? It makes a lot of sense to have 1 folder with 1 CSS file, 1 JS file and 1 PHP file for each shortcode, don't you think?