My Mac Book Pro Safari and Settings Icon Disappeared
This has happened to quite a few people, myself included.

I tried various methods of fixing it, but in the end the only way I managed to get any results was to reboot a few times.

It happened to me on various icons over about a week but then after one certain reboot they all came back and I’ve had no issues since.

You’re more than welcome to try methods discussed online or on other questions here, but none of them worked for me personally.