for me there are two legitimate options regarding the "unavailable" coins
1) confiscation by some authority (most likely after all the stuff i read) - short and long term extremely bullish
2) he lost the private keys (even thogh supply is much shorter that is extremely bearish due to the public picture that even the oldest exchange cannot handle the technical issues around the currency, how should average joe do that?)
and one option that does not make sense
3) 840k (!) coins are stolen (without noticing), that is almost 1000 coins per day since the time mtgox is operating
There are probably some other variations here.... HOWEVER out of the variations that you describe, it does seem number 1 is the most likely..... .. but there could be some variation or combination of 1 and 3... ... or like some of the fiasco situations that are described in which there is a partial loss that was back in 2011... and then GOX et al... gamble and lose with investor's BTC b/c they are in fiat at times, such as november 2013... when BTC prices are doubling and tripling...