I'm way late to this party, if anyone is even still here (the chips are kind of stale, TBH) but in my defense, I only discovered the thread earlier today, anyway, so …
Now that I'm using the EN desktop app, I decided to adapt the first script in this thread for AHK v2:
#Requires AutoHotkey v2.0+
#Warn
#SingleInstance ; Only 1 instance of the script can run
; Purpose: Open, Minimize or Make active the Evernote desktop app
; Evernote handler
*^#e::evernote_handler() ; App - Evernote Desktop: Minimize, Activate or Start
evernote_handler() {
static _exe := "ahk_exe Evernote.exe"
If WinActive(_exe)
WinMinimize(_exe)
Else If WinExist(_exe)
WinActivate(_exe)
Else Run("Evernote.exe")
}