There are many articles on the internet about folder best practices, but there are few that are actually accurate in their assessment. This is mostly due to the idea that a folder structure is the ideal way to build out a SharePoint site. Keep in mind, the reason a company moves from a shared drive to SharePoint is because employees find it hard to use, both in organizing and finding documents. So why would you rebuild the same structure somewhere else? When making the move from a shared drive, the new platform should be structured to keep employee frustration to a minimum and documents from being saved on employee computers.
A folder structure presents problematic organization, such as documents with so many versions that it is impossible to know if the document being edited is the latest and greatest, too many folder separations for documents, or remembering where to find documents you need to edit. SharePoint allows us to change the way we find and save documents, with an incredible amount of extra functionality not available on shared drives. For us to get this functionality, we need to avoid folder norms, and create a better structure.
Best practice for folders is to only use them for security purposes (permissions), so that documents that need to be seen only by authorized users are kept that way. This, in conjunction with metadata, makes for being able to quickly find anything with a few clicks, instead of drilling down through too many folders, only to find you went the wrong way. There are exceptions to the rule, but they are far and few between.
When building libraries in SharePoint, the command for adding folders should not be available to anyone outside of the company power users that are building the libraries, as users will add folders regularly, if given the chance. Once the folders are set, for security purposes, the folder command should be turned off, as it is available by default in newly created libraries. Check out this video on how to turn off the folder command in a SharePoint library: