How do I disable this message: "the disk was not ejected properly"?
This applescript will close them for you. Paste it into Script Editor and then Save as an application. Then grant access to that application in (System Preferences > Security &amp; Privacy > Accessibility)
Then you can use an application like ControlPlane https://www.controlplaneapp.com/ to run the application on wake thus closing them all automatically!
** Note: You will need to grant Accessibility access to ControlPlane as well.

tell application "System Events"
tell process "NotificationCenter"
    set numwins to (count windows)
    repeat with i from numwins to 1 by -1
        tell window i
            set temp to value of static text 1
        end tell
        if temp contains "Disk Not Ejected Properly" then
            click button "Close" of window i
        end if
    end repeat
end tell
end tell