They give several well-considered criticisms of the question - it leads people to focus on socioecomonic status, it doesn't correlate with other measure like whether they report experiencing joy recently, etc. It's not much of a defense to simply say "well, it's the standard".
My criticism is about how the dramatic language differs from the banal content of the article.
Titling it "The World Happiness Report Is a Sham" and calling it "beset with methodological problems", I would expect some more serious scientific malpractices, like data fabrication, calculation errors, sampling problems, p-hacking, etc., not "I think there are some problems with this variable".
Disagree. Whether I'm entirely fabricating data that claims A by writing numbers into an Excel sheet, or whether I'm doing a survey that measures B and then claim it means A, isn't materially different in outcome. The outcomes are just as bad, and that's what people care about. Maybe you as a researcher care that the former is more immoral, but to everyone else it doesn't matter.
I think there's a difference in outcomes between fabricating data, and getting data that still remains validly gathered, but measures something subtly different.
And I think the general public can make meaning of that
difference and have a stake in both – in the same way that the general public knows that stock market values and economic security are different things, even though people still have a lot riding on retirement plans based on stock investments.
Is joy related to happiness, or are they two separate concepts? That depends on your cultural background and the languages you speak.
The World Happiness Report can be traced back to the UN General Assembly Resolution 65/309, which was proposed by Bhutan. Therefore the intended definition of happiness in this context is similar to the one in Bhutan's Gross National Happiness index.