This article is pretty unfair to Fama.
For one thing, they don't mention any of the work he did showing that value-based approaches beat the market. Of course, pointing out that he actually did significant work showing that you can beat the market would completely destroy the narrative of economics enamored with EMH and unable to even entertain the idea that it is false. Well, the most famous proponent of the EMH though you could beat the market, so I think this narrative is just a strawman.
I also think the article is unfair at criticizing Fama for saying "I don't even know what a bubble means". I, too, would love to see a precise definition for what a bubble is. If there actually were a generally accepted definition for "bubble", then there would be little little room for argument about when we were in one. Instead, it seems like, for each of these bubbles, there were plenty of people arguing at the time that we were not in one.
Finally, the article seems to be implicitly suggesting that, if the EMH were true, there would be no big drops in prices. (I think, by "bubble", they just mean "big drop in prices".) But this is simply a misstatement of what the EMH says.
Later in the article, he gets more precise and says that big drops happen much more often than predicted by the EMH. This admits that big drops are not inherently inconsistent with the EMH. However, the claim about how often big drops should occur does not come directly from EMH. E.g., EMH can claim that stock prices are taking a random walk, but you can't say how often big drops will happen without assuming a particular probability distribution for the walk. I would bet that he's saying a random walk using a normal distribution predicts big drops are rare. But I would also bet that a random walk using some fat-tailed distribution predicts big drops are not rare, so I do not think these facts really contradict the EMH.
If you really wanted to refute the EMH, you would need to show that you can predict (beforehand) that big drops are about to occur. It's not enough to predict that big drops will eventually occur; you need to give a timely prediction.
I would love to see real evidence that big drops can be predicted. Not just because we would learn something (the EMH is false) but also because I could use that information to short stocks and make big bucks! Of course, once I start doing that, the drops would go away. In fact, if anyone had figured out how to predict drops, then the drops would have disappeared already. And that's basically why people believe in the EMH in the first place.