Like @ryanjamurphy, I keep my notes in standard file formats (typically HTML for me, so that I can use rich-text features like multiple highlight colors and text colors, but also lots of diagrams, spreadsheets, etc., in other standard formats) in my computer’s filesystem and index them in DEVONthink (v2), with heavy use of file tagging. I never edit the content of files in DEVONthink, but use “Open with…” (usually “Open with default editor”, keyboard shortcut: shift-command-O) like @tonycraine and @ryanjamurphy to edit files in my preferred editors.
I also use Leap.app, Finder, BBEdit, and Terminal to browse/search/batch-modify files. This is another benefit of using standard file formats in the filesystem: I can use a variety of file editors and filesystem interfaces. I suspect this gives me more control than the “obscured database” approach that you mentioned as the alternative.
I’ve been happily working this way for about five years and I don’t anticipate changing.