The first option seems to be the most possible one out of the three. It is virtually impossible to crack the encryption. If they are indeed capable of cracking the encryption, then the value of Bitcoin will become close to zero. And the second option is also very unlikely. Because I don't expect the hackers to be some noobs, who would use compromised emails or simple passwords. It looks to me that the hackers were in a hurry to cash out, and they sent a part of their stash to an exchange where it was seized and handed over to the FBI.