What's wrong with traditional file shares?
SharePoint is best for Office docs. It's not great for anything else, especially binary files, or files that link to other files. And you'll probably run into file lock issues if they're edited by multiple people.
If there's a clear delineation you can use for separate sites, use it. For a ~40 person business we just had one site. For a ~4000 person business we had one for each business unit. It's just an additional layer. Quantity of files and folders could be a factor, depending on how much you will be using it.
Also, if you're in any kind of regulated industry, keep that in mind.