Interesting, I didn't take that into account - I rarely work with file manager.

Shared media is a network storage. I just picked up a lot of file from it. You have no mSD, right?

I guess, it is because MyDoc now is treated differently and it has no special meaning, so any directories with name starting from '.' (dot) are hidden.

I am not sure that it has a sense to find a solution for this...

BTW, "Photo" application now shows a huge number of files. Most of them are icons but I unexpectedly found some photos which I never recognize! It seems it is some application backgrounds (like 'stellarium').
It seems it also has the same problem - some pre-configured directories now are different.