The reason I disagree with this argument is that it boils down to "tons of scams are better than a few sophisticated scams because users are more wary."
Users themselves have various levels of sophistication, and unsophisticated scams have plenty of victims.
The only reason I disagree with your disagreement is because Apple is making money here, and they have every incentive to turn the other cheek. Their entire business model is based on driving user interaction and spending, so I don't think they're the most trustworthy party to audit the App Store. That would be like if we let the President decide which news channels were allowed to broadcast at the beginning of their term.
If we restrict Apple's incentives to be purely monetary, then we have to wonder if the reputational damage is less than their cut of users being scammed.
I would argue that the reputational damage is worth more, strictly monetarily. Apple is an incredibly valuable brand, estimated in the hundereds of billions of dollars[0], and they are understandably protective of it. If <2% of the top 1000 apps are scams (from the article), and Apple periodically catches scams and helps unwind them (2/3rds of the apps the Post reported were removed), I don't think Apple is making all that much money here. Remember that Apple does't keep its 30% cut when a transaction is refunded.
The reputational damage is worth more only if there is reputational damage to begin with.
There may have been some smaller isolated stories in the past, but the truth about App Store scams is really only now coming to light - and so Apple’s calculus might be changing.
I don’t think it’s unreasonable for Apple to know who is publishing apps and making money off them in order to facilitate law and order in cases of flagrant illegal activity such as this, and for users to assume there is accountability that deters the behavior.
Users themselves have various levels of sophistication, and unsophisticated scams have plenty of victims.