I've even had experiences where I was profoundly affected by some interesting material, only to later realize that I had encountered that material (in a different book) less than a year prior. I hadn't ignored the material the first time, and had been affected by it then as well. I'm pretty sure it didn't shape me at all.
Whether to take notes or not depends on the purpose of reading nonfiction. When I read biographies, I'd like to get the bigger picture rather than the details - so if I do take notes, they are very sparse (e.g. summarizing the major points - perhaps 1-3 pages worth). With some other books I copy quotes of insightful points (e.g. reading The Demon Haunted World, I was struck by how critical he is of the behavior of many skeptics, and noted the irony that many skeptics had recommended the book).
But when it comes to potentially useful self help books: There's really no point in reading them if you don't take serious notes. They don't make for great reading, and may actually have useful material for you for life.
Books like Gladwell's: They're mostly for entertainment. It's fine not to take notes, although it's probably better to read fiction itself.
His response (immediately before much of your quote) was: "They spend all this time highlighting and analyzing. I read for interest, right? What I really remember is that people have to write 250-page books, because that's like a publisher rule. It doesn't matter if you have 50 pages of ideas, or 500, but you can tell pretty fast. I've read some really good books that are only 50 pages, because that's all they had. You can also read 50 pages, and you think, ‘wow, it's really great!’, but then the next 50 pages is the same shit. Then you realize it’s just been fleshed out – at that point I wish they just published a shorter book."
That doesn't sound like books that take more effort to really understand (e.g. Plato's works). In more technical subjects, such as mathematics textbooks, would it really be possible for most students to thoroughly understand the subject by just reading, without note-taking or at the very least, trying the practice problems? There is certainly value in note-taking for subjects and books worth thoroughly understanding, even accounting for edge cases where students can learn complex subjects just by reading, without writing.
We're shaped by unconscious gestalt understandings, not by small details.