Are they manipulating the market using your deposited bitcoins/USD? Perhaps.
Do they still have all the BTC/USD in their wallets/accounts that they say they do? Probably.
Does anyone know for sure? Nope.
If you want absolute security, don't use an exchange. AFAIK, none of them have independent audits verifying integrity, so you must realize the risks when you trade or keep money on any of them. At this point, I'd probably trust crypto exchange more than MtGox though... they seem to strive for transparency and quick response, neither of which MtGox is good at. CE just needs to establish a track record now, and they could do very well.