While Herbert's screenplay wasn't used, he actually had quite a bit of involvement in the movie and actually did rewrites with David Lynch on the script. One such rewrite shortened the script by 15 pages and saved the budget 15 million dollars (you do the math). He could've gotten a screenplay credit but declined out of respect for Lynch.

Herbert's level of involvement kind of helps to ignore things like the weirding modules, but as a friend of a friend of mine replied, "Frank Herbert was also drugged out of his mind in the last years of his life. What's your point?"