Personally I think the article posted by the OP was using the link baiting strategy of stirring controversy.
True, most directory links are lower value than sources that are more unique, have a better pattern of of links to themselves, and have a lower link density per each page. A link in a random SEO directory won't be nearly as effective as a related site to yours with a high link portfolio to itself.
But directory links absolutely have an effect.. else Google wouldn't still themselves recommend DMOZ.. and if you doubt that, try using a few crazy long-tail terms to link to your site in a directory, using words not otherwise mentioned, and watch your site rank for them in the SERPs.
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