How do subdomains affect SEO and why are they rarely used?

Question

Search Engine Optimization

There was a question of the correctness and profitability of using subdomains on their sites. I noticed that many sites like Vkontakte, Facebook, Odnoklassniki, Pinterest, Habrahabr do not use subdomains.
First, I would like to explain how I use subdomains in my projects. For example, there is a site with a purely farming theme, with articles, a gallery section, discussions and a store. The site has 5 topics, for example: pigs, sheep, cows, rabbits, chickens. In reality, the topics diverge very much, despite the fact that the audience of visitors for each section will be different, and the site system itself is identical.
The question arises: Which is better to use theme.site.com or site.com/theme in terms of SEO?

Answer 1

All this will be one site
site.com/theme
site.com/theme2
site.com/theme3
And these are already different sites
theme.site.com
theme2.site.com
theme3.site.com

Answer 2

and I have a question in a similar topic:
On reg.ru hosting, cPanel creates technical domains like domain.u0587810.cp.regruhosting.ru on which the same site opens as on the main domain. What to do with it? deal with it or what?