This weekend there has been some new information about the missing Mt. Gox bitcoins from a japanese Bitcoin security specialist called WizSec.
Most or all of the missing bitcoins were stolen straight out of the MtGox hot wallet over time, beginning in late 2011. As a result, MtGox operated at fractional reserve for years (knowingly or not), and was practically depleted of bitcoins by 2013. A significant number of stolen bitcoins were deposited onto various exchanges, including MtGox itself, and probably sold for cash (which at the bitcoin prices of the day would have been substantially less than the hundreds of millions of dollars they were worth at the time of MtGox’s collapse).
You can read the full investigation at the source here:
An interesting read!