Also, there are varying money laundering laws that look a lot like those limits.
for instance, the in the United States, only CASH deposits (or withdrawals) of the arbitrary amount of $10,001 or greater are subject to any "limit". Cash meaning printed federal reserve notes. Not anything electronic, or check, or anything.
And this limit means simply filling out a federal form stating that this transaction happened. (Currency Transaction Report, CTR)
there is no limit or prohibition to those large amounts. but it is a crime to not have the CTR done or to try and avoid it via structuring.
Mt Gox is in japan right? I dont think japan has more restrictive cash controls than america, if any
there could be some regulatory issue - such as the OP mentioned - liquidity, fractional reserve