Where your website files and pages are located on your server doesn’t make any difference to your SEO. However, where your files and pages are located on your website, and how easy they are to find by search engine spiders, does make a difference.
Search engines judge page importance by where they are in relation to the homepage. So, a page that can be reached in one click from the homepage is deemed more important than one that can be reached in three, for example. When creating a website structure and adding pages to your website, remember that all pages should be reachable in three clicks from anywhere on your site.
Old SEO articles may tell you that where filed are located on your server does make a difference, but this was never actually the case.