What I want to know is: Do all the contradictions in TrekLit (and TV/film Trek too, I guess) really bother anyone? Has anyone’s reading actually been ruined because Novel A said so-and-so about Kirk (or whatever) and Novel/Film/Episode B said otherwise?
It depends. If a TV episode or movie happens to contradict what happened in a book, that's a minor annoyance. As long as the book and the movie/episode are both good stories, I can live with it. For a lot of practical reasons, filmed Trek takes precedence.
The Crucible trilogy disregards a lot of stuff established in other books, but that was intentional, and for a reason I can buy into. The stories were more than good enough to make up for the contradictions.
It does bother me that PAD's characterizations of the new TNG characters were so different from KRAD's. In an ideal world, the editor would have made sure that the characterizations were more consistent. Maybe there just wasn't time, I don't know, but it did bother me.
It bothers me that there's one minute of canonical screen time for Captain Bateson, establishing that he has at least two female bridge officers and is not in the middle of a crisis, and Diane Carey's Ship of the Line ignores that. She just has to be consistent with a tiny little bit of filmed Trek, it's all she's got to build on, and she ignores it, presenting Bateson and his all-male crew frantically fleeing a Klingon attack. But there are plenty of other reasons I dislike that book.
So... it depends. It doesn't necessarily ruin a book for me, but it can annoy me.