I would rule that the first shuriken to hit would get sneak attack damage... The other hits would get none...
It's still a great weapon for rogues... If a rogue throws three shuriken, misses with the first and second, but hits with the third, he still gets his sneak attack damage... Pretty good for a class with a medium BAB that wont always hit...
Also remember this is a ranged weapon, so it can only be done once or twice while your opponent is flatfooted... Invisibility is a different story, but that grants its own bonuses...
I had totally forgotten about the scourge!... Is that printed anywhere besides the old Dragon article?... My rogue is definitely going to find one of those ASAP...