Tried using %%sitename%% in a Custom Post Type archive title template, but output showed my tag as it was "%%sitename%%" instead of replacing it. I looked through the code and patched it.
Joost, please see the info below and patch in your next version - thanks!
$title = $options['title-ptarchive-'.$post_type];
$title = wpseo_replace_vars($options['title-ptarchive-'.$post_type], array());