the speedrun to the end happened because originally it was supposed to be a two part movie - the first draft is the proof - more or less like the Villeneuve movies ending with the Harkonnen takeover and then switching to Atreides comeback in the sequel. Dino was on board with that and then Universal who paid for it said "NOPE" so the story was remodeled into one movie long movie and thats how it went into production. And then the test screenings went badly and the movie got reedited into a two hour running time making it even less coherent.

the "Secret nukes" were in the book

Secret Nukes were always a thing. The family atomics were used to destroy the shield wall to Arrakeen in the final siege, they don't really explain how they managed to keep them though to my rememberance. No one seems to know how to resolve the whole lasgun+shield=even bigger explosion thing though. Something I thought for sure they would have used when Harkonnen raided the Atreides occupied palace in the new movies since it happened in the books.

Either way big explosions are cool regardless of source.