MagnificPopUp is not a function

and where does your jQuery load : in the footer?
Try to load your script above as

add_action('wp_footer', 'enfold_customization_add_magnific_handler');

and what should the popup script do?
maybe a midclick : true can do the trick:

add_action( 'wp_footer', 'enfold_customization_add_magnific_handler' );
function enfold_customization_add_magnific_handler() {
  ?>
  <script type = "text/javascript">
  jQuery(document).ready(function() {
    jQuery('a[rel="magnific"]').magnificPopup({
      type: 'inline',
      midClick: true,
      preloader: false,
    });
  });
  </script>
<?php
}

by the way: do you have an older child-theme header.php ? The lightbox setting on that has changed – so if you got – actualize this with the newest one.
________
On Enfold ( i do not know it this is default setting ) there is a setting to load jQuery in the footer – so that was the reason for my question.
If you load that script in the head area.

So – to understand it right. You go to your menus and on one or more items you set with rel = magnific

first the selector is wrong – i did not see it first too on your code above. ('a[rel="magnific"]')

then – what do you like to open? do the menu-items lead to a unique ID on that page – or do they have as target a website ?
f.e. if you like to open a website with that link then type : ‘iframe’ , is to use.