If you read their documents, you will see that Mt Gox STILL does not understand that customer deposits are NOT "assets of Mt. Gox". It is a complete shit show and I cannot wait for the perp walks because maybe that will wake some idiots up that this is not a game.
Depends upon who holds the deposits. Some brokerage firms have a third party Trustee hold the Customer Deposits. In that instance, the customer deposit is never an asset of the Company, and will not show up on the Company's financial statements.
However, there are some companies, like utilities, apartment complexes, etc., that hold customer deposits in their accounts. Even if the accounts are physically separate, they are under the control of the Company. As such, they are company assets with an offsetting liability. Thus, they show up on the Company's financial statements.