Generally speaking, combining all of the global scripts will boost performance, but so will enqueueing JS selectively – meaning if a script is only used on one CPT or template, you should only enqueue it there.
Look into conditionally enqueueing JS in your functions.php. You can target specific sites by blog_id and target specific post types, templates, etc. If some of your JS is very short, you can also add an inline script rather than serving a separate file. For example:
function wpse_306134_enqueues() {
// enqueue the sitewide theme script file
wp_enqueue_script('wpse-scripts', get_template_directory_uri() . '/wpse.min.js', array('jquery'), '1.23', true);
// enqueue an inline script only on the 'about' page
// adjust this condition as needed: if is_singular, etc.
if(is_page('about')) {
wp_add_inline_script('wpse-scripts', '(function($){jQuery(document).foundation();})(jQuery); jQuery(".gallery-icon a").swipebox();');
}
}
add_action('wp_enqueue_scripts', 'wpse_306134_enqueues');
Personally, I would put all my JS files in a single folder and name them by blog_id if that applies. It may make sense to have a global JS, then site-specific ones, and then these additional inline enqueues for small snippets that don’t apply to most URLs.