Here's my $0.02:
I think that these two companies probably made decisions, but not completely based on SEO or organic ranking.
The Mic.com site that is using sub-directories will likely see much better SEO, because all of the content is on the same domain, and not treated differently.
My assumption for the Vice.com site is that they want to have different channels or content on other subdomains.
My hunch is that for Vice.com, they decided to go with subdomains, so that they could have this content live on different physical servers or different infrastructure.
I took a look at the main site, www.Vice.com, and it's using Tumblr, running on AWS with Elastic Load Balancing.
For the Munchies.vice.com, it's running on WordPress.
While it is possible to have content displayed from WordPress on one subdirectory and Magento on another (by either installing both applications on the same server, or creating virtual links behind the scenes) a lot of companies will opt to do this on separate systems.
That's probably the reason that they went this way.
In the end, SEO doesn't trump everything...
But, here's a reference about sub-domains vs. subdirectories on Moz:
In the past, I've answered a similar question in the past here: http://moz.com/community/q/blog-on-subdomain
But the gist of it is:
store.mydomain.com --> content on the store. is treated as a different site, and SEO efforts (content, inbound links, social media) only help the subdomain.
mydomain.com/store --> subdirectories are usually the way to go. All of the content, inbound links and social media shares will help build the overall domain authority for you.
My recommendation is to go with the sub directory (mydomain.com/store/, and there are a whole lot of articles that back this up:
http://moz.com/community/q/blog-on-subdomain-vs-subdirectory-best-practices
http://www.mattcutts.com/blog/subdomains-and-subdirectories/
http://moz.com/community/q/best-place-for-a-blog-blog-mydomain-com-or-mydomain-com-blog
Hope this helps,
- Jeff