Kodric says that the vast majority of holdings are kept in "cold storage" making them inaccessible for quick online transfers and therefore theft, but the attackers managed to empty out Bitstamp's operational wallet which is used for day-to-day transactions and site business.
Although on a much smaller scale, the theft brings back memories of Mt Gox, which was once the largest exchange until it was pillaged with hundreds of millions in Bitcoins stolen. The site eventually shut down.
Source:
ZDnet