My Kontakt content is split up into directories by publisher/producer, then by Product. Which I have to do now when I add things/move things. nki/.nkm files stored in %LOCALAPPDATA%\Native Instruments\Kontakt 5\QuickLoad I've often considered building some tools to manage the Quickload links, so you could have a list of directories that you wanted maintained in the Quickload and it would remove the existing dir and rebuild it fresh. On Windows (not sure on Mac) it's just a bunch of directories with file links to the. The biggest problem with Quickload is it doesn't update if you move/change things. I think the way this new Kontakt works will be just fine, it's just different. NI has been steadfast at reserving that for products that pay license fees.
Quickload is the right answer but users do seem to like having things show up in the Library list.