Since I switched to desktop, I keep tabs open on my browser and just refresh them. Sometimes I barely click off the map until I need to check alliance-related stuff or profile check.
Until I do, I don't know if I got a message. Would it be possible to display messages when received, at the bottom of the map similar to how chat shows the [!] marker? Perhaps a [1 mail] icon on top when there's a new unread email?
Cheers
Loving this game more every day! What a great strategy simulation. 
