There is the problem of one document not necessarily being one file. Sometimes you have sidecar files or some meta data that is stored somewhere else in a database of sorts. So it can be messy, especially dealing with antiquated formats like dcim (easy file name conflicts), gopro leaves extra thumbnail files scattered around, wtf is even DS_STORE, etc etc. I also think that file managers are not powerful enough for searching and managing all kinds of data, the fact that we need photo management software proves it.
It's not perfect, but the macOS way of creating "bundles"; where a directory looks like a single file if it has a particular extension is 99% of the way there. The average user double-clicks and it opens in the relevant app. The power user can right-click and choose 'view contents', which opens it like any other directory.
This can also be done via compressed files with an application-specific extension. We use it at work for Python zipapps, and of course everyone probably knows .docx and .xlsx
> file managers are not powerful enough for searching and managing all kinds of data, the fact that we need photo management software proves it.
I don't want to be responsible for manually managing all my photos, copying them off cards or downloading from online services or whatever. I also want to view the photos in various ways: I'm regularly browsing them via the map view, or person tagged in an image, and so on. Hence the photo management software that handles all that for me.
But the photo management could certainly be better integrated into the OS, ie open your Photos folder and rather than seeing raw image files, it would load the photo management.