I've just installed Admin Menu Editor (following Phil's advice) and noticed that "Subscription" menu item added to user menus when Pro Sites is active, doesn't appear in the Menu Editor. I mean, the menu is visible to users, they can operate it just fine but I cannot modify the item in Menu Editor as it is simply not there.
Not sure what is causing this strange behaviour ... I've done a bit of my own digging, tried Membership to see if that works as expected, and it works just fine. Membership menu is visible in Menu Editor and can be modified as expected. Site Wide Text Change also works just fine, modified menu items are seen in the Menu Editor and can be moved/altered. So it looks like this "disappearing act" is only limited to Pro Sites.
Saying all that, this is not a big issue. "Subscription" menu item itself works just fine, none of the functionality is lost. So, I guess I just wanted to see if someone else is seeing the same.