The Fifth Amendment initially applied only to the federal government, including the Due Process Clause of the Fifth. Most of the Fifth Amendment has been incorporated and is applicable to the states and their political subdivisions through the Due Process Clause of the Fourteenth Amendment. So, most of the jurisprudence talking about due process under the 5th is incorporated in the 14th. The requirement that a grand jury return an indictment (5th amend.) has not been incorporated via the 14th.
While technically, the judge was correct that the 5th doesn't directly apply to Honolulu, most of it is applicable through the 14th. I don't know exactly the context so this may not be a real issue anyway.