As someone who knows what goes on in libraries, archives, and antiquarian bookshops, I will give a short explanation, which is two pronged. Marking with stamps serves two purposes: evidencing the ownership, and deterring potential thieves.

The stamps, as shown by the case you linked, can mark who is the owner of any given book, or which institution does it belong to. This is important both for matters of cataloguing, and for historiographical reasons. The traceability of ancient books can only go so far in certaing cases, but having this type of record is good for researchers. I'll give you an example: in the library of Wolfenbüttel they have a particular specimen of the novel "La vida de Lazarillo de Tormes y de sus fortunas y adversidades" printed in Lérida in 1612 by Lluís Manescal. This book can be traced to an auction held in the early 19th century when one such specimen was available. Is it the same? Yes, the previous owner had marked it on the inner cover of the book with his signature. This type of mark would have disappeared in the case of a crafty thief, which takes us to our second point.

Deterring of thieves. The traceability I just mentioned would have been gone for good if a crafty thief would have taken the binding out and substituted it with a new one. If the marking is one the pages "defacing" them even a bit, not only would it lower the selling value, it would also make the book virtually impossible to sell.

Some engravings are worth a lot of money by themseslves, and that would make them very attractive for thieves: they are something easy to obtain with a scalpel blade, and can be hidden inside a notebook. The stamp defaces the engravings, and marks the ownership, making it evident for everyone that they are stolen goods. This why I, and my bookselling friends, recommend to use the stamp on absolutely every single woodcut, copperplate, or drawing present in any book. It may be the simplest and cheapest way to deter a potential thief.