Well in my own opinion.. Yes, it's wasted. It's much better if the author will know that what they write will truly impact the Trek universe. Something I really appreciate now with Star Wars. They check every litterary work but once released, you will know that this really happened.If you enjoyed the book, is it really wasted? The Final Reflection is one of the best Trek books ever written, but was completely contradicted by Next Gen. Does that make it a waste?
As I already said and seem to make some people upset, and I apologize for that, but a book which isn't canon is worth just as much as fanfiction. Sure the quality might be better but the impact is exactly the same.
Take The Final Reflection. A great book but the story is meaningless.