I do hate to see library books vandalised, though I have sometimes use pencil in my own property.
Sadly, as with everything, people who get a free service show no respect.
It seems a very long time since I borrowed a book from the library that has not been marked "discreetly" by regular library users.
From what I notice, people choose to put a dot over a particular page number, or monogram somewhere, often on the front or back cover, and they always use biro.
I assume they do it so they can check if they have read the novel before, or not. Whatever the reason it still defaces library property!
Passports not in the drawer I always keep them in. Turning the place upside down.