Because Mt. Gox is a corporation organized under the laws of Japan. Corporations in Japan can own many things of value, such as hotels, laser printers, intellectual property rights, Alpha Black lotuses, swiss francs, and promises to be paid in the future... but all of these things exist, on their books, with a yen value next to them.

In the event of a bankruptcy or civil rehabilitation (民事再生, which is what Gox is going through IIRC), creditors generally get paid out in yen, not in cement mix, even if the company only happens to own cement mix.