Well, it doesn't have to be a reference to a Kelvin film. We're just interpreting it that way. Something else (perhaps with similar consequences) could be in store for the novelverse.
The novels can't contradict screen canon. The fate of Romulus in 2387 is part of the canonical history of the Prime universe, and the novels have to stay consistent with that history even if they can't mention every part of it. So they can't make up some similar event to take the place of the canonical one.