Jeri Taylor referenced her own novels in Voyager. I have nothing against it, as long as it's done carefully and for a reason. If Shatner's novels get referenced I'll probably facepalm.
Though it's safe to say any series set post Nemesis is probably gonna screw over a lot of novels.
STO? It's a game loosely based on the novels and I don't even see it being relevant to comment on.