EDIT: Pathfinder Ninjas do not add their wisdom bonus to anything AFAICT.
That aside, whether "wisdom" is a bonus type is debatable, but ultimately irrelevant. You only ever have one wisdom bonus, so there is never another bonus of the same "type" for it to stack with (or not). You cannot add a single bonus twice, any more than you can claim arbitrarily high bonuses to attack rolls by adding the bonus from Weapon Focus multiple times (okay, that would also fall foul of the "same source" rule, but there is a fundamental reason than that why you cannot do it).