Yet another mysterious move by Nintendo.
The Pokemon Bank application has been removed from the "Pokemon X and Y" feature on the Nintendo 3DS' eShop. You now need to manually search for that application to find its page.
Nintendo most likely removed that convenient link because some fans have been stressing the eShop servers to find out if Pokemon Bank is available for download.
Speaking of the 3DS' eShop, Nintendo are offering The Legend of Zelda: Four Swords Anniversary Edition for free from Thursday, January 30, 2014, at 9 AM (PST) until Sunday, February 2, 2014 at 11:59 PM (PST).
Update (January 31, 2014): Joshua Edwards in the comments below reminded us that we can add Pokemon Bank to our eShop Wish List for faster access to that applications store page.