This is quite an interesting dilemma in more than one way. While Nintendo has a positive net income (below the bottom line, which includes all transactions, ie. money made with exchange rates, etc), the company has an operating loss of $220 million (making hardware and software costs more than the revenue from them). While this may seem like it doesn't matter since the company did get income, the income didn't come from the place it should have come from (software and hardware generated revenue).
Also this is expected revenues, it's not final. Still, just like any company, lowering sales expectations by around 20% is generally not good. The biggest problem I see here is what will happen in the future in regards to the operating profit. Depreciation of the yen can't be done multiple times or Japan will have more problems due to other countries doing the same and making the process pretty much moot (it's also debatable that China has been doing this for years according to the US among others).
The same situation can be seen in quite a few financial statements during the last few months. Nokia for example had a positive year, but it wasn't due to its core functions (phones), but instead the networking part NSN (Nokia Siemens Network). Just like Nintendo, it's profit, but not from where profit should be made.
