The only ownership stake we know about (and the details kinda slipped out) is Creatures, with a 10% stake.
It is “intentional” insomuch as Game Freak created Pokemon as an independent developer, Creatures stepped in to help finance the original when GF was struggling and took a producer credit/cut. Both of those developers being independent is because it’d cost Nintendo a LOT of money to buy them out, given the value they generate, which Nintendo would likely not have anticipated until well after the fact. They are able to keep them close because they hold shared copyrights/trademarks on Pokemon and, because that doesn’t cost them as much as a purchase, they are OK with that. Why spend money if you don’t have to?
Game Freak and Creatures, because they make the money they do, likely have current management that have no intention to sell, no matter how interwoven their fate is with Nintendo at present. But that won’t necessarily last forever. When Tajiri, Sugimori and Watanabe are ready to retire and sell Game Freak and Ishihara is ready to sell Creatures, Nintendo will have to shore up the cash to make it happen, and as I said, it will not be cheap, unless Pokemon as a franchise sees a massive collapse.
The same principle applies to HAL, IntSys and Camelot. Not spending the money to acquire has freed up cash for other things, but there will come a point where the money will be spent on these teams, likely with a similar trigger event.