NDCube was a start-up subsidiary conceived by Nintendo and their ad partner Dentsu. Nintendo had controlling interest 79% from day 1, so it was always a subsidiary. Dentsu eventually sold their shares back to Nintendo, but it didn't change much.
The notable change came when Nintendo retooled Monegi (a Nintendo joint-venture with Hudson) and hired several former members of Hudson, to basically restructured the entire staff and direction of NDCUBE.
I feel like the Nintendo late 1996-2000, was a time when Nintendo was starting and investing into a lot of companies.
Nintendo Start-Up Companies
Randnet, Monegi, Mario Company, Mobile 21, NDCube, Nintendo Software Technology, Nintendo Software Canada, Marigul Management
Nintendo Q-Fund
Genius Sonority, Alpha Dream
Nintendo Minority State Investments in Affiliates (20-25% equity)
Silicon Knights, Left Field Productions, Rareware, Retro Studios (which was soon after bought out by Nintendo), HAL Laboratory (which was later sold back to HAL when Nintendo and HAL did joint-venture Warpstar)
I would argue Nintendo Pictures and Monolith Soft are on a similar level of going from some minor history to unexpectedly becoming subsidiaries. There are several Japanese companies with an extensive history of contracted work and assistance like Eighting, Grezzo, Good-Feel, and others that are currently independent and still freelancing/commission to other publishers.