Apple can't deprecate the URI standard. It sounds like they've simply stopped using it for links between apps. The actual article title is "iOS 9.2 Update: The Fall of URI Schemes and the Rise of Universal Links," which is a lot less breathless.
Given the title and intro, I expected information useful for people not using the app. Skimming the article didn't yield any, I was wondering if I should bother reading the article if I'm not interested in their app.
I had to solve this problem a couple of years ago for transactional email links from a startup that later ran out of money. It's useful to know that Apple has an alternative solution to linking directly to an app now, or that there is at least a third-party service to help (even if this post is self promoting).
The title should be updated to match the article, though (it's currently "Apple Deprecated a 7 Year Old Standard Today").