Mesta on Eldre'thelas has an interesting tale of woe over on the forums: he had someone within his guild ninja a few items from the guild bank, and then they discovered the next day that the guy had "disappeared" completely-- he not only didn't appear on their server, but he didn't show up in the Armory, either. Metsa thinks name change, and that appears to be the likeliest scenario-- not a lot of reason to ninja valuable items if you're just quitting the game with them. So it looks like yes, name changes will simply let ninjas run free.
Blizzard's official response in the thread is pretty apathetic-- Bornakk basically says that you've got to be careful about who you let into the guild bank ("l2bank," essentially). Over on Massively, we recently posted about something called "MMOrality"-- the idea that players uphold a social code in game. But that's all based on each player having their own identity, and the premise that if someone does something wrong, you can hold them responsible for it. But these paid name changes, it seems, takes away that little bit of justice-- if we can't hold players responsible for their actions at all, we can't enforce MMOrality in any way.
Blizzard still can-- obviously, they know who's who even if names get changed. But just the same, I'm not sure if players should necessarily have access to name changes-- the majority of people who change their names have legitimate reasons for doing so, I'd guess, and it's a shame to let the few ninjas ruin everything. Is there a way we can allow players to pay to change their identity while still making sure those who break the "MMOral" laws are held responsible for what they do?