This honestly seems like an accident.
If when you click an app link you choose "Choose Application..." in the modal that pops up, you can then click "Options", then in the "Enable" dropdown choose "All Applications", the choose "Evernote". And the link works.
So the code that accepts, parses, and sends you to a note based on the link is all there and working.
The issue seems to be they forgot/overlooked/didn't get to registering the URI scheme with macOS so the OS knows to shoot those links automatically to Evernote.
If true, this is a very simple fix. Hopefully they'll get on it soon.