Nintendo's got lots of money everywhere.

Also, think of it this way. Numbers are made up to make things a little easier...
Nintendo sells a system in Japan for 25,000 Yen. When they launch the system, there's a (fake) exchange rate of 125 Yen: 1 Euro - so this translates to about 200 Euros... so they put a price tag of 200-250 Euros on it.
Four years later, the exchange rate is now 75 Yen: 1 Euro - putting that 25,000 Yen system at 333 Euro... but, of course, Nintendo can't just start raising the price of the system in Europe... they have to lower it - it's older, after all.
So, all of the stock they have built up in Europe, all the holdings, everything they have in Europe is now worth (made up numbers again) 37% less... and Nintendo can't just jack up prices to make up for it.
Of course, in this case, we're dealing with a 4-year old system - how much has the Euro dropped since the 3DS launched? *and* Nintendo just did a massive price drop on the 3DS. Not only did they lose money (assets, really) there (a warehouse full of 1,000 $250 3DS units - $250,000 just became worth $169,000), you also have to factor in the costs related to the dropping currency exchange... (again, made up numbers) - 1,000 3DS systems that are in a NA warehouse at launch are worth $250,000 - or, let's say an exchange rate of 100 Yen:$1, the warehouse is worth 25,000,000 Yen. Now, we drop the price and the Yen gets stronger, say 75 Yen: $1, that warehouse is now worth $169,000 - or 12,675,000 Yen. Bamn - doing nothing but sitting on stock, you just posted a 50% loss. Obviously, the price drop was Nintendo's "fault" - but the changes of the Yen vs. other currency isn't really something they can do much about.