Hi @cognaccola,
This is probably because the shortcodes are not applied to the title and/or the excerpt. You will need to add additional code to the functions.php of your child theme, if your SEO plugin does not apply shortcodes directly on specific parts. You can do this by (for example) writing something like this:
add_filter( 'the_title', 'do_shortcode' );
add_filter( 'get_the_excerpt', 'do_shortcode' );
and so on for other texts filter hooks.
Additionally you may check at your SEO plugin what are the filter hooks for their title, description, open graph, etc.
Please let me know if that helps.
