Magisterial judges tend to be lower-level judges, but court officers (e.g., lawyers) still address them as "your honor." It seems, given the title of their office, that "your majesty" would be the most appropriate form of addressing the office. Has that ever been used? If not, are there logical or historical reasons it has not?
tl;dr: The terms have separate etymologies. Majesty derives from greatness, while magistrate comes from mastering something (people or a trade).
Middle English (in the sense 'greatness of God'): from Old French majeste, from Latin majestas, from a variant of majus, major.
Also, c. 1300, "greatness, glory," from Old French majeste "grandeur, nobility" (12c.), from Latin maiestatem (nominative maiestas) "greatness, dignity, elevation, honor, excellence," from stem of maior (neuter maius), comparative of magnus "great" (see magnate). Earliest English us is with reference to God; as a title, in reference to kings and queens (late 14c.), it is from Romance languages and descends from the Roman Empire.
Latin magistratus ‘administrator’, from magister ‘master’. This also gives us master (Old English), its weakened form mister (mid 16th century), and miss.
Also, late 14c., "civil officer in charge of administering laws," from Old French magistrat, from Latin magistratus "a magistrate, public functionary," originally "magisterial rank or office," from magistrare "serve as a magistrate," from magister "chief, director" (see master).