There's a similar question: How true to the original vision of Frank Herbert were the sequels published by his son?
Many Dune fans have a problem calling the last 2 books, Hunters of Dune and Sandworms of Dune and the other books by Brian Herbert and Kevin J. Anderson, canon with the original 6 books.
Quality of these books aside, there are some discrepancies that many readers cannot accept:
- Daniel and Marty
The final chapters of book 6, Chapterhouse: Dune, introduces us to two mysterious characters called Daniel and Marty. Their conversation seems to indicate that they are Face Dancers who have become independent of the Masters. However, in book 7, they are revealed to be Omnius and Erasmus, the leaders of the thinking machines.
- The Butlerian Jihad
Frank Herbert described the Butlerian Jihad more like a religious and philosophical revolution to ban the use of computers instead of a physical war between humans and machines. Frank Herbert may never have invented the character Omnius. However, since Frank Herbert never elaborated, we don't know the details of this event.
- The Golden Path
The Golden Path was necessary to ensure humanity's survival. In book 4, God Emperor of Dune, Leto says humanity would already be extinct if it weren't for him. This means the threat that was going to end the human race was internal. It is implied that the destruction is caused by "seeking machines", but where do they come from?
On the other hand, there is the "Unseen Enemy" that scared the Honered Matres back into the Old Empire. Who or what is this Enemy? Frank Herbert never told us.
There are other things, but it's been years since I've read any of these books.
I do believe there was an outline for book 7 written by Frank Herbert. However, that's all it is: an outline. I'm sure Brian Herbert and Kevin J. Anderson had to fill in a lot of blanks. What is easier than to delve into the prequel books they had already written?
I believe Brian Herbert cares about his father's work and made a genuine effort to finish it.
Officially, these books may be canon, simply because they say they are.
But they are probably not what Frank Herbert intended. You can either accept it as canon or see it as a separate work based on Frank Herbert's work.