Based on the "Behind the Scenes" series, cross platform font support is being addressed in upcoming beta releases, but apparently by significantly restricting the number of fonts we are allowed to use within Evernote. This is expected and probably
I'm not a huge font user, but I've come to rely on Source Code Pro for mono-spaced text as I'm often dropping in code snippets or similar examples where it's not always possible to guess the correct character based on context.
I would encourage you to carefully select which monospaced font is to be made available, such that every character is readily distinguished. Courier New is a poor example, as seen in this sample screen shot taken from my Mac and the current Evernote ver 7.13.