Sometimes I use subfolders and sometimes I use files. I have not been able to decide if there is any real benefit (in terms of ranking boost) to using either. A lot of CMS these days use subfolders in their file path, so I am pretty confident Google can deal with either.
I used to prefer files like .html when I was building a new site from scratch, as they were the ’end of the line’ for search engines, as I imagined it, and a subfolder (or directory) was a collection of pages.
I used to think it could take more to get a subfolder trusted than say an individual file and I guess this sways me to use files on most websites I created (back in the day). Once subfolders are trusted, it’s 6 or half a dozen, what the actual difference is in terms of ranking in Google – usually, rankings in Google are more determined by how RELEVANT or REPUTABLE a page is to a query.
In the past, subfolders could be treated differently than files (in my experience).
Subfolders can be trusted less than other subfolders or pages in your site, or ignored entirely. Subfolders *used to seem to me* to take a little longer to get indexed by Google, than for instance .html pages.
People talk about trusted domains but they don’t mention (or don’t think) some parts of the domain can be trusted less. Google treats some subfolders….. differently. Well, they used to – and remembering how Google used to handle things has some benefits – even in 2016.
Some say don’t go beyond four levels of folders in your file path. I haven’t experienced too many issues, but you never know.