I suppose there could always be a DTI novel that references the fact that in an alternate timeline Romulus was destroyed.
If that happened, that would totally spoil Star Trek. I'm sorry, but it happened in the prime universe. Not some alternate universe. So the books should be depicting the destruction of Romulus. While Pocket's main Trek line is not allowed to play in the alternate universe, this is not an event that took place in some alternate universe. The books don't have to pander to Countdown
. But Romulus getting destroyed is something that has to happen.