The response code is still the default and the external links are still valid.
But I think with your last point we might be narrowing things down. There are half a dozen weblinks on the site but only three were singled out by Google. Based on the network tab in Chrome developer tools, I think the issue is coming from a subdomain redirect which only exists for these three weblinks.
We setup some subdomains as a shortcut to the external sites. These MODx weblinks are directed to the subdomains which in turn are also forwarding to the external site. I’m not sure how that creates a soft 404 for Google, but it seems like it has to be related.