Heh, well you've moved the goalposts a bit by assuming four sets of controllers in your calculations. There's no way that Nintendo is going to include four pairs of controllers in their standard $200 bundle. (actually it wouldn't surprise me if Nintendo tries to push the price up a bit now they know how expensive the opposition is going to be, but I digress)
But even taking that into account I'm still not finding your figures even remotely plausible. You have to appreciate the economics of manufacturing electronic devices. The vast bulk of the overall costs go towards research & design, marketing, and distribution. Once a production line has been set up in some Chinese sweat-shop the costs of making the actual physical devices is a pittance. It wouldn't have cost Nintendo significantly more to have come up with fully wireless controllers.
Also, where are you getting the idea that the base unit would require an additional four ports? A standard bluetooth hub supports up to seven wireless devices, so assuming Nintendo can't work around that limitation, only one extra hub would be required. And remember, this is cheap off-the-shelf technology. Even Jakks is now selling wireless plug & play games.
So why the cord? I can only really speculate. Perhaps Nintendo decided that people would prefer the hassle of a cord over the hassle of having to charge two separate sets of batteries per player in order to play games. Perhaps, as you mention, form factor was an issue. Maybe there is another technical reason we just don't know about. But whatever the reason (or reasons), I'm convinced that Nintendo's decision was based on design considerations rather than cost.