I am playing on a Mac. This is a totally unmodded new game I just started to test this issue, which has never used any mods.
I placed a family of previously saved sims, two of whom were already Arch Dukes into a new world. The crown menu in the new world showed the Arch Dukes as nobles in the world. The game was saved in live mode.
I deleted the whole sim family while in the sims manager. The crown menu showed this:
I saved in live mode, and exited the game. I opened the game again and navigated to the world. The crown menu showed this:
Adding the same family back into the world did not delete the llamacorns. It did add the new Arch Dukes, but the llamacorns remained.
I was able to start another new game and repeat this by following the same steps. The game will not allow for the complete deletion of noble sims. Something still persists.
The same thing happens to the crown menu if you delete the default noble sims in the new world.
I did a little troubleshooting after discovering the problem:
Using testing cheats and cas.fulleditmode to enter CAS, I was able to rename a noble sim in CAS without it causing a problem. I was able to change a noble sim's facial characteristics and alter the noble sim's body without it causing a problem.
I was NOT able to substitute a noble sim by changing the name of the substitute to the name of the original noble sim while deleting the original noble sim (that resulted in a missing noble sim in the crown menu and family tree, but it did not put a llamacorn placeholder in the crown menu or an unknown in the family tree).
I discovered that evicting the sim family did remove their names from the crown menu without a llamacorn placeholder. But the game is still tracking them into a new world if they are moved. So the problem continues to exist. They should not be deleted.
I did discover a "fix" for the noble problem. Have every noble sim abdicate: they instantly become non-nobles. Their names are removed from the crown menu. If they are moved to other worlds, they will not appear as nobles in that world's crown menu.
(And because they are no longer nobles, I am guessing they can then be deleted like any other non-noble sim in the game, but that is only a guess because I cannot see what happens at a code level. However, I do NOT know what it will do to a previous family tree or a dynasty if they are deleted as non-nobles. Deleting them as non-nobles is a separate issue I did not test, as yet.)
Until this is fixed, probably the safest way to remove the default noble sims from your game completely is to kill them and send their ghosts to the nether world. But to be safe, have them abdicate first.
If, as a result of my bug report, they fix this glitch, the problem may not be retroactive to already saved games. So if you value your save, do NOT delete noble sims.
Edit By crinrict: Added pack tag to title.