This has to do with the way we package the product. The messaging part is not displayed as a separate menu item. However you can send system message to users by finding them in "User Management. Here you can send to all or send to selected.
You can also administer a certain user's direct messages by clicking the users username in the search result. Look at the "My Direct Messages" tab in the pop-up.
I just flipped through the Functions Descriptions manual and looked at chapter 1.3 - Contact/Messaging function. Then I took a look in my EC 3.1 admin interface, and there is no menu item for this function. Have I overlooked something or is there a bug somewhere? I have added my own menuitem, but hardly think I have deleted an existing menuitem (althoough this is entirely possible).
I'll install a new 3.1 installation and have a looksee, but in the meantime - can someone clarify if there is a bug, config or whathaveyou?