They are! Very clearly old books that are being well taken care of because of the age. Some have had copies made for archival purposes, but they, too, will have those missing pages. They will also be able to see those indentations so it will be obvious the pages are gone.

As for symbols, YES! There are! But to be fair we'll only allowing Sherlock to find at least two for now: a spiral and wavy, squiggly lines. These symbols will also be very minimalist, like hieroglyphics where it's mostly lines and circles.