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.
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.
Should we also fret over the life of a bank robber being ruined when they get caught? Whose fault is it that they chose not to make an honest living? There are risks involved when you decide to take short-cuts in life by profiting off of things you have no legal right to.