If some of your comments will contain shortcodes and some won’t, there’s no harm in running them all through do_shortcode(). If the content has no shortcodes in it, it will simply be returned, and if it does contain shortcodes, they’ll be parsed and the content returned.
So you should be able to change
echo '<span>'.$comment_content.'<br>';
to
echo do_shortcode( '<span>'.$comment_content.'<br>' );