I have the same issue with the same AppGameKit Studio version (2020.11.12) in Windows 10. The media folder is there in the project, but it's not displayed in the Project Window.
But I can't see the folder opening the project in the explorer too. I have the Steam version.
In Mac version works OK, and works OK in the Windows demo version (?).
I tested with many example projects and I create a new project in another folder, but no media folder is displayed.
I deinstalled the program and reinstalled again, but I have the same issue.
Project screenshot is attached: