Pikmin 3 Wii U digital copies appear to have potentially gone extinct. The Nintendo eShop and official site no longer show a “buy digital” option for the game. This happened on August 5, 2020, the same day Pikmin 3 Deluxe was announced for the Nintendo Switch. Nintendo itself has yet to issue any comment about the situation. [Thanks, Nintendo Everything!]
The product pages for Pikmin 3 remain online in North America, Europe, and Japan. The demo download also is still available in each region. Also, it is absolutely still possible to purchase other Wii U games digitally, like The Legend of Zelda: Breath of the Wild and Paper Mario: Color Splash. (Even Tokyo Mirage Sessions #FE, which received a Switch port, is still available.)
However, there is a precedent for this happening. Donkey Kong Country: Tropical Freeze was removed from the Wii U eShop ahead of the Switch port. If you search for it on Nintendo’s site, the only version that comes up is the Switch release.
The Pikmin 3 Wii U version is immediately available physically worldwide. Pikmin 3 Deluxe will come to the Nintendo Switch both digitally and physically on October 30, 2020. GameStop is still selling Pikmin 3 used physical copies for $19.99 and new digital copies for $59.99.