Had the exact same issue with Chrome on my Mac. It was set as the default browser and correctly opened when using hyperlinks in all my apps, except Evernote. It was correctly set in the system preferences as "Google Chrome.app" was the selected choice. In order to fix it I had to do the following:
Set the "Default web browser" to "Safari.app"
Open a link from within Evernote (it opened Safari)
Change the "Default web browser" to "Google Chrome.app"
Open a link from Ev