I was watching Freakonomics the other day (well, part of it, anyway), and they were talking about how the Japanese police will only really investigate crimes when they have a clear chance of getting a conviction. Take that as you will, but it seems to be that even if there's an investigation, that doesn't mean that anything will necessarily come out of it.
That and the Japanese police also will try to get a conviction even if it means convicting someone with little evidence. Combined with their seeming incompetence at investigating cyber crime this does not bode well for the MtGox investigation. The Japanese police have a 99% conviction rate with prosecutors being fired for threatening to kill suspects if they don't confess. The Japanese system of "Justice" strives for convictions, not justice.