Just to pick a nit: Classic mode is "native" -- it's just boxed into Mac OS X, and a system that "boots" OS 9 is no more native than one that's running classic, it just has fewer other things to fight with, both in terms of application software running reliably and consistently and in terms of the system's resources.
Plus, if somebody does get OS 9 booting directly on a G4 mini, it'll likely be missing platform drivers, making it unstable, or GPU/ethernet/sound drivers, making it unfun to use.