All this is MY opinion, not WoTC's opinion. Ask WoTC for their opinion if you wish, but their opinion is still an opinion. Ask the DM to have some spine and make his own ruling on the subject. That would be the correct answer.
IMO, tossing 3 shiruken is essentially throwing 1 "primary" shiruken that has all the deadly effects (poison, sneak attack, flaming, wounding, etc) plus 2 "secondary" shiruken that just do 1 point of damage without additional effects. The only effects I would apply to the secondary shiruken would be magical, weapon focus, or masterwork bonuses (and if it has returning magic they will return).
The set of 3 shiruken attacks are considered a single attack for game purposes. So any factor which would provide an additional attack would yield an extra 3 shiruken attacks (1 primary, 2 secondary). So a fully-proficient Rog3/Ftr16 with Rapid Shot is quite capable of hurling 15 shiruken a round! However, the +2d6 sneak attack, his weapon specialization bonus, and most other effects would only count for 5 of them.
Some may disagree with me nixing the poison or special magical effects like flaming on secondary shiruken attacks. However, I generally follow a policy of "there shall be no cheap exploits involving shiruken use". Attack bonuses are not cheap exploits, but most damage bonuses (except those paid at full cost for enchantment bonus) are.