Some fans have speculated that the 24th century events of Romulus being destroyed and such from Star Trek 09 are another alternate universe, not the one in which TNG/DS9/VOY have been set. So I suppose the novels don't have to see it as canon and make sure events lead up to it.
Except that "some fans' speculations" and "canon" are two things that have nothing whatsoever to do with each other. A few fans' opinions have no bearing whatsoever on the policies of Pocket Books and CBS Consumer Products.
As a rule, tie-ins are obligated to stay consistent with what's onscreen. Sometimes tie-ins aren't allowed to mention
something from a given series or film if they don't have a license for it -- for instance, Marvel's 1980 Trek comic not having a license to include storylines or characters from TOS that weren't in TMP (although it managed to sneak in a ton of TOS references anyway), or IDW not having a license to do Voyager
comics (although they managed to work Tuvok into The Last Generation
anyway). But that still doesn't allow willfully contradicting what's onscreen.
Granted, on occasion, tie-ins have been permitted to reinterpret what was onscreen, to acknowledge what was shown but to offer an explanation for it that differs heavily from the original intent -- such as the way the novels retconned Trip Tucker's apparent death. The filmmakers' intent was clearly that Spock Prime is "our" Spock, a direct link from the old continuity to the new -- otherwise there would've been no reason to include him in the films or do the time-travel story at all. However, going strictly by the letter of the text, it might be possible to rationalize it as a Spock from a different timeline -- or to assert that the Prime timeline split in two sometime between Nemesis
and 2387, with the supernova happening in one branch of the timeline but not in the other for some reason. So I suppose hypothetically something like that could be done. Whether it's likely to be done, whether CBS would approve it, is another matter. And whether it's desirable is very much open to debate.