Aside from shallow, uncritical notes, consider that annotating in a margin is evidence that a reader is actively engaging with a text.
Very often when I write in margins it's to question or argue against what's written (e.g. "really? what about ...", or "no, contradicts ...") which, to me, seems in line with the dialectic process Socrates promoted. Multiple sides, truth-seeking.
Sure, having a spacious notebook on the side is even better. But it's the same goal, isn't it? Engage more deeply with a text and encourage questioning as you read it, while it's still fresh.
Sometimes you have the drastic misfortune of someone totally off the rails writing crazy crap in it though, or a 3 year old experimenting with crayons. Not what the Stephenson article is about, but that sucks.
Amazon's used prices are usually set by booksellers that base their prices on stuff like this for some books... When you get to like old cheap paperback romances though, or that .01 plus shipping, you might or might not.
I would be pissed if I expected a clean, un-scribbled-on book I wanted and it was represented as such, but got that.