Here's the short of it, and of course the ending of the book will be spoilt if you read further...
I can imagine that the notches on the Gerritszoon punches could be a sort of cliched device for solving a code in detective stories. I'm not familiar enough with the detective genre to be put off by it, and I thought the key to the code was kind of clever in this way: it wasn't going to be solved by an algorithm. You had to be a curious human being who went and looked closely at the punches.
One of Sloan's overall points (if it's ok to say that a novelist has a point in writing a novel--I'm actually not all that comfortable insisting on "points" that a novelist is trying to make...) seemed to be that the Googlers who go around Googling everything can only capture some of the dimensions of reality, but not all of them. Like creating the visualization of the bookstore. Googlers are only digitizing the surface of things and mining data from surface dimensions. There are dimensions to reality, physical and especially psychological reality, that
Or even creating the physical replica of the log book. That wasn't done by Googling Googlers, but it was crafted by paying close attention to the surface of the book. It had no depth to it. Penumbra was able to sniff it out and actually used the word "simulacra," which is a loaded lit theory term that has to do with this philosophical issue in the novel.
So getting back to the Gerritszoon punches, it seems to me that Sloan is setting up a contrast between what you might call surface reading and deep reading. Googlers can surface read the shit out of almost anything, if you can digitize it. If you can turn the words of a book or the physical dimensions of a bookstore into a digital representation then you can extract information from that data. But again, you can only extract the information if it can be represented digitally.
There is also a connection here with the discussion of Old Knowledge and Traditional Knowledge that was discussed during the protagonist's (I forget his name already) first visit to Google. But since this is "the short" of my thoughts, I'll stop here.
So I guess those are the main observations I wanted to make. But perhaps everyone else who finished the book also picked up on those themes and still thought it was a bad ending.