Nice job on the digital restoration. Most likely the photos were tinted using something like these Peerless dyes; they've been around since the late 1800s and are made today. I found some vintage ones and was astounded with how well they blended into a B&W photo (done in chemistry in a darkroom).
Peerless Black & White (Dry) Handcoloring Dye Sheet (Complete Edition Water Color Book) - 15 sheets | Freestyle Photographic Supplies
I don't know of any pens ever used; pencils - yes, those were used I think in the '50s and 60s. I don't know the original size but it would be well, maybe impossible! to trace the eyeline in a photo precisely. I think it's more likely with longer exposures done with earlier cameras that the black parts of the image were black enough to stand up over time, maybe more noticeably than the lighter gray parts. Could be that, or the type of lens, or paper used, etc. - too many variables to know for sure.
You can see where the paper was cut/torn how yellowed/brownish it is. The original paper would have been off white. So the color probably looks somewhat different than it did originally. Of course that adds to the vintage look of it!