It sounds like they optimized for the wrong thing.
You can take your Hannah Barbara example as proof that some intangible things have an aesthetic impact, but you still can say when you see the two cartoons that one seems to be of better quality -- I hardly thing that is 'subconscious'. I think this article is intended to focus on the things designers do that are stylish yet unremarkable or wholly unnoticed, which any sensible designer must agree is something of a problem for web designers.
Now, it works because of the HB cartoons' light-hearted style and premises, but would seem tacky and ridiculous for a film or episode attempting something grander (i.e. a feature film like The Little Mermaid or Toy Story).
[1] For example, many HB characters don't have necks, or have extremely thick necklaces or collars where a neck would normally be. This allows you to swap out head and face animations with much greater freedom, and makes it harder to detect camera errors when the head and the body don't quite line up correctly. Is that bad? Not necessarily, but if you rely on too many of these tricks you end up painting yourself into a corner.
[2] Also, some HB characters don't even walk correctly. Their torsos and upper bodies stay perfectly motionless while their legs flail about beneath them. It looks cute and storybook-like in certain applications, but completely ridiculous in most others.
The fact of the matter is that people usually do notice, if only subconsciously. If you show someone a clip from a Disney movie and a clip from a Hanna-Barbera cartoon, they will be able to tell that the animation quality is much crappier in the latter. They won't be able to tell you why, but on a visceral level they will be able to feel the difference. [1]
This visceral feeling of "quality" is what gives Apple's brand such cachet. Sure, their skeumorphism can be tacky, but it's never slapdash. Their apps always run at the highest framerates, and their touch interactions and animations have always been tweaked to a level that their competitors can't match.
Now, if you asked someone what the difference was between Mobile Safari on an iPad Mini and Chrome on a Nexus 7, no one would say "the scrolling is much smoother on the iPad, and the variance in framerate is much lower as well, which contributes to a feeling of responsiveness and playfulness", but those features still contribute dramatically to the "feeling" you get when using one of the two devices.
Now, sometimes it really doesn't matter. The example in the OP seems particularly silly. However, don't underestimate the value of "bumping the lamp" when it comes to design or interaction development. People will notice.
[1] The answer to the "why" has many parts, but mostly involves the fact that Disney animation runs at 24fps while HB cartoons ran at 12fps or even 6fps. Disney animation involves characters that are carefully articulated and that move realistically and with a sense of weight behind them. Also, the general quality of animation and camera work was just better -- look, there are a lot of reasons. They all add up to the difference between Scooby Doo and The Little Mermaid.