MacOS default folders missing
I think that it's a permissions problem.

diskutil resetUserPermissions / `id -u`


After entering the diskutil command, if Terminal says that permissions reset on user home directory failed (error -69841), enter chflags -R nouchg ~ and enter the diskutil command again.

You can also double-check whether your user Library folder is set properly. Open Finder as root:

sudo /System/Library/CoreServices/Finder.app/Contents/MacOS/Finder


Now navigate to your home folder, click on Library folder > cmd+J > check the box for "Show Library folder".

Let us know whether this solved your problem.