I disagree that this view. The problem with classic links, is that they only work in the desktop app. If I try to view them on my phone, for example, they fail.
The previous behavior was best: open the link in the Desktop app if it's installed / available, and use the web otherwise. On mobile, use the mobile app if it's installed, and use the web otherwise. That makes complete sense, since presumably the reason I installed the desktop and mobile apps is that I want them to handle everything Evernote for me.
Additionally, it's a standard behavior for apps in general, for links and files. "Hey, I'm an app that can handle this kind of file, or this kind of link, so I'll open it rather than send it to the browser". It's true of other mobile apps when viewing web links to services provided by that app (Google Maps, LinkedIn, Trello, etc.), and also for Windows with default files and protocols (tel: links, file: links, etc.)
Evernote should be no different.