Change thumb's size
If you need to modify the thumbnail sizes for the posts it can be done through CSS if you look for the #items classes and find your thumbs. But it also depends on the php output. You can see what i'm talking about by going inside template-portfolio.php and see line 67:
$size = $v_columns == 'four' || ($sidebar['sidebar_type'] != '' && $sidebar['sidebar_type'] != 'full-width') ? array('220', '165') : ($v_columns == 'three' ? array('300', '225') : array('460', '345'));
This is how items are determined. You could modify these to be squares. The same needs to be done if you're using shortcodes inside the plugin (wp-content/plugins/js_composer/config/shortcodes-front.php).
Please use a child theme for your changes! Don't modify the core files directly (except the plugin where you don't have what to do), because you won't be able to update easily in the future.