Apart from the possibility of regulatory issues, if the blockchain/transaction record is hidden, then groups of pool owners of large pools could potentially collude to double spend, and if there is no transaction record, then this will not be detectable. Other such scenarios exist as well - remember that the blockchain is a public ledger designed to prevent or record fraud. Hiding this exposes the coin to serious risks.
The only anonymous coins that will hide the blockchain itself is zerocash, which hasn't even been released yet.
Monero/Cryptonote doesn't hide the blockchain
Darkcoin/Coinjoin doesn't hide the blockchain
You can still see what pools have what hashrate, double spend attacks, etc on Cryptonote coins and Coinjoin coins. Zerocash is the only one where the blockchain itself is hidden and you can't see anything at all.
And there are ways to regulate anonymous coins to prevent fraud/money laundering, via the exchanges they're traded on, just like USD/EURO etc etc on Paypal
As far as i know dark hinders to detect the source and destination of payments within the network so making it hard to identify wallet addresses and following transactions through the block chain. So like i said earlier one of the main reasons of a public ledger is to prevent or record fraud. Hiding this exposes the coin to serious risks.
In case of MtGox it would be not possible to follow coins if it would've been with dark, or other scenarios where there is need to follow the coins.
There is no need for MtGox in the future. Smart contracts will prevent fraud and make centralized exchanges obsolete.