Well, I'm obviously just guessing here but I think that the friend-stuff is Nintendo Network related so the friend list they're using makes use of that. I say that because Nintendo Network is basically their big picture online roof that houses everything (eShop, Miiverse, etc). The NN logo is on all the game boxes that use online (Ninja Gaiden, Scribblenauts, etc). The friend data should be taken from that even though you may or may not "connect" via Miiverse.
I understand the family tree like this:
.......................................................................................|---> Mii Plaza........... |---> Miiverse
Nintendo Network..(basic features: Browser/Friend List,etc)...|---> Nintendo TVii
.......................................................................................|---> eShop
all of these should be able to talk to each other (we know NTVii can access Miiverse) and access data from each other but they all operate under the bigger Nintendo Network umbrella.
What we also know is that
ZombiU will use uPlay (all Ubisoft games do these days so no surprise there). But I think it would be crazy to assume they'd use those accounts for their online features. You traditionally link your platform-account to your uPlay account so it always accesses the uPlay account automatically if you have done so.
I'm trying to find a way to phrase the two ways Miiverse is used but it seems finding a clear expression is very hard. When I say "does not actively use Miiverse," I mean in the way NSMBU and supposedly Nintendo Land will use it. Integrating Miiverse INTO the game directly (see: NSMBU map screen). When I say "has access to Miiverse," which all games do, I mean the activity feed thing that you can call up from the Wara Wara screen that shows you what people are saying about the game and who is playing it right now, the basic systeml-level stuff.
The same thing he did last time, would be my guess?