No. They didn't hook up on Innocent. It's just the same old: she's the most important and especial to me. And they use the word "friend", because they don't know better, even if everyone tease them about how much they like each other.
That's what was covered but it's not the whole story, remember that Vivio traveled back to the future in this manga and she tries to avoid calling Nanoha and Fate their mothers because it may change the future, which implies that not only Nanoha and Fate in Innocent will start a relationship and form a family like in StrikerS/Vivid, but that also Vivio may be their biological daughter in this timeline.