To my experience that folder gets created automatically when you install (and launch) DEVONthink 3.
Ever since starting with DEVONthink 1, I always had my databases placed in folders that I created at locations where they fit for me. When I recently installed DEVONthink 3, I recognized that folder you mentioned in my home directory, but it was empty. So I assume you made your installation in september last year and that’s when this folder was created.
Yes, the Databases folder is created when DEVONthink first launches. It is a convenience location for people who don’t know where to store their databases, or a place to relocate them when needed.