It depends on the time period you're modelling. Up until the Battle for Leyte Gulf, her wood decks--which were Hinoki cypress--were natural wood. Hinoki cypress is very light colored, lighter even than teak, and would have been kept holystoned and bright. However, both Musashi and Yamato stained their wood decks black for the Leyte operation, using a mix of funnel soot and oil. Yamato's decks were still stained black when she was lost.
Cheers,
John Snyder, White Ensign Models, http://WhiteEnsignModels.com