Nintendo profits hugely from business external to consoles... i.e. other-media Pokemon, The Seattle Mariners (Nintendo owns a majority share) etc.
I always find it odd to compare those numbers directly to game division profits from Sony and MS. Pokemon has been a huge boon to Nintendo for the entirety of this, and last console generations. The Mariners are a huge sports franchise, and have been quite profitable for a long while. I believe the profits from all those sources are included in reported profits in the links above...
Isn't comparing those profits directly to console game divisions a bit... spin, in favor of Nintendo? Heck, Sony uses their game division to bolster their income for their BD, UMD, & DVD disc and drive royalties (yep Sony gets royalties from DVDs... not a lot though), and disc manufacturing divisions as well (they "pay" other divisions for the goods/services/licenses, showing as a loss on the games division, and a gain for the other divisions). MS profits hugely from their accessories (PC keyboards + mice, which sell like hotcakes), which is included in their EDD profits, etc. -- its just not as simple as the raw numbers make it seem.
In short, the GameCube was not as awesomely profitable as it first appears, from Nintendo's financials... as if that were Nintendo's only source of income during those periods. Heck, the GBA alone would have dwarfed it, if the 'Cube was indeed profitable at all.
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