I wish I knew what samurai did, there is no clue at all in game as far as I know.
Substance abuser is a prerequisite for substance addict trait - which gives -2 to all stats, but I haven't seen that one happen. Trait currently AFAIK is only on Kenji Doihara, which is a reference to his heavy opium addiction.
Samurai Lineage is a trait that is used in one of the Japanese focus tree paths (basically all generals with this trait side with one side). It was also said during pre-release that it should increase the Banzai tactic frequency used by generals with this trait, but it seems not implemented or removed before the release (it was decided against it during development)