The Magnakai disciplines do not state that they provide an increase to the saves. Since the text doesn't, I can safely assume that it means that they don't provide any bonuses.
Think about it - the Kai has all saves at +9 at level 20, without the +5 bonuses (which takes them to +13 - more than any other class).
Do you really want any PC running around with +19 saves? :shock: