I'm also very annoyed by desktop notifications now showing up for every event I have in my calendar. I just disabled all desktop notifications for Evernote and EvernoteHelper, cause I couldn't find a way to just disable these "create note" notifications for calendar entries.
On MacOS open System Preferences – Notifications – Evernote / EvernoteHelper and disable Allow Notifications from Evernote
It's pretty terrible UX cause now I probably won't be getting some important reminders, but unfortunately I didn't find another way.