The widely used Spring Framework and its module Spring Data JPA encourage using queries the way I described

That’s new to me. Can you show me a reference where this is explicitly stated?

This repository method generates a Hibernate query and makes providing departments mandatory (empty list returns 0 result, null returns IllegalArgumentException).

Because this implies that nobody encourages this kind of usage.

Spring 5 (with Hibernate 5) made it easy to provide optional departments:

I’m sorry you based part of your application on something unspecified which just happened to work in this particular case, but like I wrote before, this kind of query is very inefficient. Don’t use that. Go the extra mile and implement proper conditional filtering.

With Spring 6 (including Hibernate 6) I have to implement it via Criteria API and Custom Repositories, which is more costlier and verbose

You don’t. I’d suggest everyone to use Spring Data Specification here for this purpose.

@Repository
public interface UserRepository extends JpaRepository<User, Long> {
  @Query("from User u " +
         "where COALESCE(:departments) is null or u.department in (:departments)")
  default List<User> findAllByOptionalDepartmentIn(
                @Param("departments") List<Department> departments,
                Sort sort) {
     return findAllByOptionalDepartmentIn( (root, query, cb) -> {          
          return departments.isEmpty() 
            ? null
            : root.get("department").in(departments)
      }, sort );
  }
  List<User> findAllByOptionalDepartmentIn(
                Specification<User> spec,
                Sort sort);
}