Do they even possess 12 million?
It's quite likely that they have nowhere near that. The amount doesn't really matter as long as it's enough to ruin the accused. It's possible that they'll declare bankruptcy and Nintendo will take much less than that, perhaps even a fraction of the total. Everyone involved would be aware of that when the settlement was proposed.
The point is really to send a message that they are willing to destroy someone's life over this.
That's the part that I hate, that they're claiming this "caused Nintendo irreparable injury." I would have been okay with it if the settlement had been simply to close down the website forever plus the seizure of all assets used in its operation.
Most people will never get to own a 1961 Ferrari 250 GT California Spider, but I don't think it would go over well if I opened up a car dealership called "Love Stolen Cars".
Terrible analogy. If a car is stolen, then the owner loses the use of that car, plus any ability to sell it or make a profit on it in any way. A better analogy would be if someone started making replicas without permission.