Jodorowsky been very weird about whether or not he read Dune. He probably didn't read it when the project was brought to him - but he definitely gave it a close reading afterwards. He wasn't going in blind - that's for sure. The script is out there and it shows that he had way more than cursory knowledge of the book and its lore. He gave most of it his own twist and propped up a lot of rituals and symbols but in its core it oddly close to the book conceptually and even goes slightly beyond towards a territory covered by the latter books. he even kinda gives the story a sort of morbid happy ending.