I would agree, kind of. As a website owner, clicks were all I was interested in as far as adverts were concerned. They were how I got paid, after all. As long as they didn’t offend/annoy my readers or interfere with my actual site content, I wasn’t really concerned with what they were showing. Just as long as you clicked on it. If you didn’t then purchase whatever the advert was selling, well not my problem.
But yes, the advertisers themselves could maybe stand to learn a lesson that clicks aren’t everything. Unfortunately, the real life lesson they’ve learned to date is that ‘annoying, obtrusive and downright shady adverts get the most clicks’. Like I say, we as users have to take some of the blame for that - it’s no good just allowing the good adverts to be shown - advertisers and publishers don’t care. Everyone needs to engage with them as well. Click on the ones that interest you, buy the products if they suit you. That’s the only way that decent, non obtrusive adverts will ever take precedence.
I’d agree. But, while the bigger companies have more complex, customised setups, the majority of smaller sites will use an ad service such as Google Adsense or similar - it looks like the site you linked to uses these such services. These don’t offer a lot of control over what ads are displayed - you can select what formats you want and you can usually block specific categories or specific ads, but you don’t otherwise get a say. If a new advert suddenly starts being served up then you won’t know anything about it until you see it yourself or someone complains about it.
Going the other way, I used to have a lot of problem getting harmless, but not overly relevant ads to show on my site. If adsense couldn’t come up with ads that were relevant to my content, usually it just wouldn’t show anything at all. Again, as a publisher, not much I could do about that.
Considering the state of most sites whenever I surf without adblock, I wouldn’t say it was much of a secret. 
QFT. The worrying trend (I call it a trend, but it’s been going on for a few years now) is for the less scrupulous advertising partners (taboola, to mention just one) to format their ads to look the same as the parent site, trying to fool users into thinking they’re just clicking on a link to another page in the site.
Nope, pretty sure it was deliberate. I never allowed any adverts that looked anything other than what they were, I never allowed popups, mouseovers or anything like that. Sure, a few people probably did click accidentally, but certainly not due to anything sneaky or underhanded on my behalf.
Advertisers have got this down to a precise science - to the point where they can predict what parts of a web page you’ll look at first, where your attention will stay the longest, and what size, shape and format of advert you’re most likely to click on. It’s to the point where Adsense (the Google advertising service for websites) will tell you off if they detect that you haven’t placed adverts in the most optimal positions of your site.