I see this exact issue a lot as well when consulting with customers. It isn't so much a startup problem as a website problem, when a site is over-designed and not built to sell.
It's interesting that a lot of people equate the modern world to slavery, but this is the first article I have come across which partially agrees with that assessment and still challenges it. I think it is correct in assessing that slavery is not quite right (we have moved on) and yet there is still more work to be done for freedom.
there is plenty of free software which is up front about including ad's, which is the ethical way to offer free software and get paid to do so. Also, this is not some software that was developed as free, but often pirated themes/modules/plugins modified and then billed as free to put in ads.
Also, one of the links in the article does show many of these echo'd. In some cases it is a lot of javascript, in other pure links.
As for proof, you are right, it is possible these guys are using unethical SEO firms instead, but I still think they should be monitoring and dealing with this issue. In some cases, there are thousands of backlinks which have similar footprints. I have trouble buying that they are blissfully unaware.