The chrome headlight doors have identical raised edges that align with the swage line that begins at the headlamp door on each front fender, continues on the door and disappears near the rear of the rear fender. There are no right or left headlight doors, so the vestigial swage line commonly called a "notch" was introduced onto the opposite surface of the headlamp radius on the fender to correspond to the raised edge of the headlamp door so it would not look out of place.
. . . More than likely they were sanded off, which is why you don't see them any more.
As others have stated, I don't understand the obsession with these bumps. If they are missing it is very easy to put them back in place so they are certainly not an indication of authenticity.
Perhaps, rather than a sign of authenticity, one should regard them as a sign of knowledgeable attention to detail when examining a restored or repainted Pagoda body shell. When the notches are missing, it may very well be taken as a sign that someone didn't know, or didn't care, that they should exist. Conversely, when they are there, it might be taken as a sign that those responsible took the time and care that they be properly reproduced and thus may have been more likely to have taken the appropriate time and care with other details as well.
In retrospect, it is probably a blessing that the bean counters at Mercedes-Benz thought it appropriate to produce a single headlamp door frame for the W113. As dear as they are already these days, can you imagine how dear they might be if we had to look for unique right and left-hand doors today?