1) There's a huge increase in valuation for their company.
Nintendo employees (especially VP and C-level) could make a lot of money off of this fact. Ultimately, that money is coming from a bunch of investors because these guys get paid in stock and stock options.
2) The investors made the wrong investment, so they'd either lose or gain money based on a false premise.
So, Nintendo is being the nice guys here by setting them straight. Their execs could've just cashed all their stock options right now and ran. Instead, they issue a statement helping to set these investors straight before they lose any more. It saves Nintendo's reputation as a long-term investment, but they also built a good will with investors.
3) Nintendo didn't need to do this
They have the cash reserves to essentially self-fund all their projects. They could've burnt through good will in the short term and made a ton of money, but they didn't. They aren't in need of investment capital and haven't been for 20+ years.
Good on you Nintendo for being an outstanding corporate citizen.