I think this question is based on a misunderstanding. I think this misunderstanding is based on two facts.
Patent trolls do try to get broad patents on existing technology and then sue others. They don't do that by patenting the prior art but by filing divisionals / continuations and fuzzy claims. Essentially they try to take an inventive idea and formulate the patent in a way that its as broad as possible. Then they wait for improvements others find and file a continuation with claims encompassing that improvement but based on the priority date of the earlier application and somehow on the wording but often not the meaning of it's text. Why? Because money.
Broad claims. Every good application will start with overly broad claims that claim part of the prior art. That is because it's easy to narrow claims but almost impossible to broaden them and it's hard to exactly know how broad a patent the examiner will allow. So you try iteratively, starting with broad. And another point is that the description of the patent has to be enabling. If it is not, the patent might get invalidated. So the description will of course have many well known aspects, just to make sure.
It's not completly untrue that people try to patent prior art - or rather - they patent minor improvements. Because having many patents is important. If another company wants to sue you and you have 20 patents on minor things they are infringing too, you can get a good deal. If however you only have one good patent, they might design around it or attack it.
One can approve of the patent system or not, but it does allow patenting of minor but inventive improvements. And that's not inherently bad. There are patents out there that should never have been granted and patent trolls monetarizing them. But the patent system isn't full of people trying to patent prior art. Because it costs money and - apparently opposite to popular believe - patent attorneys, patent examiners and inventors are neither stupid nor blind.
And of course, sometimes it costs less money to file for a patent then to do more and more prior art search. It's impossible to only file good patents.
As to your sources, the first one cites a patent "for out of office messages" without analyzing it's limitations.
From claim 1:
said first processor determining that an e-mail has not been sent from the first system to a receiver in a second system linked to the first system since said activating;
said processor ascertaining whether a current date is prior to the start date and determining, from said ascertaining, that the current date is prior to the start date;
in response to said determining that the current date is prior to the start date and to said determining that the e-mail has not been sent from the first system to the receiver in the second system, said first processor attaching the extracted availability indicator metadata to the e-mail;
So it sends messages only prior to the start date and only if they hadn't been sent, a fact your source doesn't mention. This is a very good example of said minor improvements. The website however seems dedicated to prove a point by ridiculing and oversimplifying. I don't see any real analysis there.