Menu Bar icons disappear

If after using the Safe Mode in previous suggestion and Focus suggestion and still having issues >>

1 - There could be something in the main User Account playing up. To further isolate this - Set up users, guests, and groups on Mac. Then log out of the Main User account and log into the dummy account and test again if the issue persists.

2 - If the issue is present in the dummy account - then, this appears to be a System Wide issue on the computer.

3 - If after performing each of the above steps is the order that have been presents  and still have issues - please advise for possible further assistance.

“Focus” can make things like the clock disappear. Could it be it?

Try adding them in Safe Mode, then do a normal restart: Start up your Mac in safe mode – Apple Support (AU)

Have you gone to System Preferences > Dock & Menu Bar to add them? You can also restart your machine and see if they come back.