He said that unless you have a massive number of wildcard subdomains, everything is fine.
He said this in a minute 48:24 from the video (video at the end of the article):
Question:
Can we talk about how you deal with sub-domains? We have 5. Similar themes but different enough to put them in separate folders. Subdomains were used instead. Does this affect the ranking?
Answer:
No, not in general.
Therefore, we recognize that some sites use subdomains as different parts of the site. And, in the same way other sites can use subdirectories.
With subdomains, the first thing I would keep in mind is that you are not using wildcard subdomains because that can make crawling very, very difficult. If we have to go through all these subdomains and treat them all as separate guests.
But if you have a limited number of subdomains then it could be an option.
Likewise, if you have different sites that are essentially completely separate websites but are in subdirectories – as well as folders – then let's try to account for that as well.
And well, actually they are all on the same domain, on the same hostname, but these are perhaps user-generated content – as separate sites that should be treated separately: completely, later we will try to figure out of that.
So it is not something that would improve or harm the ranking. It's more a matter of us realizing that. And so far I've seen our algorithms do a good job of that.
So I guess Google is usually smart enough to know how to deal with subdomains and subdirectories.