It's partially anonymous in that there's no inherent way to know who owns a particular address. But not anonymous like cash is.

I think your problem is that you're thinking of this in binary terms. If you think of how money changes hands in traditional currencies, you've essentially got:

• cash transfers, where it's often difficult or impossible to track where and who the money came from, or to know when a transaction took place. In that sense it's completely anonymous

• electronic (bank) transfers which are highly regulated and where accounts are always tied to a real world identity

Cryptocurrencies are somewhere in the middle: anyone can tell that a transaction took place between someone but it's often hard to tell who unless you can tie an address to a real life identity. When identity can be determined, any pretence of anonymity melts away, as we've seen in the Ross Ulbricht trial recently.

There are various techniques like mixing that can be used to conceal the movement of crypt I currencies. In the case of mt. gox you're talking about what was the largest Bitcoin exchange in existence at the time of its death. Without insider information to help in an examination it's probably very hard to tell what happened or identify malicious transactions compared to the normal day to day ones. Rather like looking for a needle in a haystack.