Intelligent Systems is a branch of Nintendo's in-house development teams, so it's really just another name for Nintendo.
HAL Laboratory is independent. They came up with Kirby and Nintendo financially aided them.
Both of your examples date back to the early 1990s. That's three decades ago and hardly indicative of how Nintendo does business now.
IS is technically independent from Nintendo actually. They aren't listed as a subsidiary on the company's press sites. If you want a more recent example, Astral Chain. The copyright notice is "©2019 Nintendo/Platinum Games, Inc."