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The game is only removing the option to buy it. Meaning there's no reason they would touch any of the other information/data on the page. It will still exist (through your download library) for people who bought it digitally to re-download it. Which means it would have to have the update data as well.
I forget how the Wii U works, but I believe updates (or notifications of new updates) are automatic. So before it boots up the game it should check for any updates and given the page will with all of the data will still be available, it should find the update data and ask if you want to update the game. Unlike something like Konami's P.T. demo which was wiped from the store entirely where even people who downloaded it weren't able to re-download it.