Which in hindsight seems extremely naïve. Files are just too damn useful a concept. Their main rival, databases, have a bunch of peculiarities that limit their generality. When people want to share information any longer than a paragraph or two, they send a file. You can’t beat files!

Of course ultimately the distinction between files/filesystems and databases is not that clearcut; I'd argue that in many ways filesystems are just databases promoted at kernel level.

I think the model they'd prefer are references. URIs to cloud resources.

That's what cloud providers want. I think users don't care and prefer whatever is the simplest and most reliable method. Cloud resources disappear all the time which tends to make a lot of users upset.

Is it discussed somewhere the ideology behind this? Users are too dumb for files? Pay extra for App Store apps just to open your own files? Prevent privacy? Security?

I think all of the above, except they won't say it in public. They'll let you figure it out. It just works.

I think layered on that, it was more the case Apple really really really never wanted to have the concept of single song music files seep into iOS, especially as it was "share with your friends" device.

The revenue stream from the iTunes Store started in 2003, well preceding the iPhone.