Hi Arthur,
There is a method called "isNativeUrl" in both iUI & Emy to deal with native URL Schemes.
Any clic event is intercepted by Emy, and go tru a list of checks, this one included.
If this method returns true, then Emy stops checks and leave the browser to handle the clic event by its own.
So the simplest for now for you is to edit emy.js & add yours in this method.
The best would be to modify Emy's code to add a addNativeUrl method so you can do this onload from your code without editing the core one.
( Github pull request appreciate :) )