The problem was that the book had so many of those cute little references in it that it became hard to tell what was new and what was winking at past stories.
But is that really relevant to the story itself? Most works of fiction contain references to events from the characters' past, even if they're standalones or series premieres. "The Cage" referred back to the recent Rigel VII battle, "Encounter at Farpoint" referred back to Riker & Troi's history, "Emissary" referred back to the death of Jennifer Sisko, "Caretaker" referred back to Tom Paris's criminal career, etc. In those cases, the viewer didn't wonder "Is this based on some earlier story?" And it wouldn't have mattered if it had been. If you're reading a Trek novel and constantly pulling yourself out of the story to wonder if each reference to the past is an allusion to some earlier novel, then you're creating unnecessary distractions for yourself. That's something to be curious about afterward, but it isn't important to know while you're reading. All that matters is whether its significance to this particular story is clear.