Wojtek sent us this thread in which he posted a long series of emails between him and Blizzard about the ninja of an Onyxia Drake. There's a lot of back and forth, but eventually, the bottom line is that Blizzard was not able to help him, whether that's because he didn't have the information right, they couldn't find what they needed in the chat logs, or they just didn't want to. Later on, the thread is locked, and Wojtek is given the usual feedback address for the GM actions.
So what does all this mean? We've heard in the past that Blizzard will occasionally help with ninjas, and we've even heard unofficially that if you get the main looter in a PuG raid to state the looting conditions ahead of time, Blizzard can go back, look that up, and then reward loot based on who really deserves it. But of course, all of that is unofficial, and there are so many variations and issues in situations like these that there can't really be a hard and fast rule -- sometimes Blizzard can help, sometimes they can't.
So basically, the one hard and fast rule that we've got is to watch your own back -- make sure the rules are clearly stated, and only go raiding with people you trust. Blizzard will probably help when they can, but from GM to GM, their policies (and the way they feel that day -- that seems to be what it boils down to sometimes) will likely differ. Ninjas happen -- as long as there's less loot to go around than people in the raid, they always will. And it's important to remember that even if you do get some loot stolen from you, and even if Blizzard doesn't help, there'll always be another instance to conquer and another drop to get.