So can you just go on with Romulus still existing?
No. We can't contradict any parts of the canon, even the parts we can't reference. They still exist -- we just can't mention them. The tie-ins are not an alternate reality to the canon. They're conjectural stories meant to take place
within the screen canon, and that means they stay consistent with it, even if there are parts of it they don't get to talk about directly. Like when Malibu got the DS9 comics license instead of DC. That meant DC couldn't publish its own DS9 comics. It didn't mean DC could pretend DS9 didn't exist.
Besides, maybe someday the license will change and we will get to openly acknowledge this stuff. If we'd just spent years contradicting it, that would put us in a hell of a pickle.
I'm sympathetic to the view that if Pocket can't reference the Bad Robot films then they shouldn't feel beholden to them in their creative and editorial decisions. If Pocket wanted to publish a big Romulan event set in 2388 -- say, the Empire becomes a Federation member and Spock is there to witness the treaty signing -- should they let something that is officially off-limits to them stand in their way? It's an arguable position.
I don't think it is.
Star Trek doesn't belong to us. We're just guests in someone else's house. If they don't want to let us into their private study, then we just don't go in.
I always approach it by asking, how would I want to do things if I let other people write stories in a universe I created, like the
Only Superhuman universe or the Hub universe? I'm protective of my continuity, so I'd want to make sure their stories would be consistent with how I see the universe. And there might be some part of that continuity that I would prefer they didn't cover because I had my own plans for it -- in which case I'd still want their stories to stay consistent with it, just by avoiding it altogether. I'd expect my ownership and creative control over my own universe to be respected, and so when I'm a guest in someone else's universe, I accept going in that they're entitled to the same deference. It's their creation, not mine. Getting to borrow it and tell stories about it is a privilege, not an entitlement. And if that privilege comes with limits, if there are lines they don't want me to cross, then that's entirely their prerogative.
You can even make the argument that the novelverse, as currently constituted, has already taken the position that Romulus wasn't destroyed in 2387; the framing device of The Good That Men Do makes no reference to the near-extinction of the Romulans. Yes, TGTMD was published before 2009, so it couldn't be written with the knowledge of a film that wasn't even written yet. But in retrospect, if you look at that book now, the absence of any discussion by Jake and Nog, in a conversation that expressly involves the Romulans, about a destroyed Romulus draws attention to itself. It is the dog that barked in the nighttime.
There are plenty of references in TNG and after to Kirk's
Enterprise being the first starship of that name, but that doesn't mean TNG is in a different timeline from ENT. Not to mention all the other details of the novelverse that have been contradicted by later canon and glossed over by later books -- like the scorpion-bodied Tholians of
The Sundered or the non-glaciated Andor of
Paradigm or William Thelonius Riker in Peter David's books or Chekov's musing in
Ex Machina about how the nature of the different races of Klingons was still unexplained. Those contradictions don't entitle us to ignore the canon we're borrowing from -- on the contrary, we're obligated to stick with canon even when it requires retconning our own prior works, because that's how tie-ins have always worked.
Besides, I just skimmed over those Jake-Nog scenes, and they were only discussing the Romulans in the context of 22nd-century events and the discrepancies between the official accounts and the newly declassified data. There'd be no reason to mention the destruction of Romulus in that context, any more than there would be a reason to bring up the atomic bombings of Hiroshima and Nagasaki in a discussion of the Tokugawa Shogunate.