Testing on a clean install of macOS Big Sur, in Terminal when I executed ls ~/Desktop
I was presented with this dialog box:
I clicked: OK
I then executed ls ~/Downloads
and was presented with this dialog box:
I clicked: Don't Allow
Executing ls ~Downloads
in Terminal again, it returned: ls: Downloads: operation not permitted
I then went to System Preferences > Security & Privacy > Privacy > Files and Folders and had the following:
As you can see what I said OK to is checked and what I said Don't Allow is unchecked.
So, check to see that System Preferences > Security & Privacy > Privacy > Files and Folders > Terminal > Desktop is checked.
Notes:
If you do not want to be prompted each time on protected folders, then add Terminal to: System Preferences > Security & Privacy > Privacy > Full Disk Access
In doing so, Files and Folders will show Terminal as having Full Disk Access instead of what's shown in the screenshot above.
If your uncheck Terminal in Full Disk Access, then whatever applications previously were under Files and Folders > Terminal will reappear with the same settings as last set.
ls -le ~
? That will show the ACL. But @user3439894 comment may be what you need.ls -l
and (as you know)ls -le
would check that the permissions are as default.