It seems that Nintendo is doing this because of Fates's unique structure. Fire Emblem Fates is an umbrella term for three different games: Birthright, Conquest, and Revelation. The story revolves around a decision made by the player character, an adopted royal facing an upcoming war, who can either side with his birth family (Birthright), his adopted family (Conquest), or can unite both sides (Revelation). For the physical release, cartridges were marked as either Fire Emblem Fates Birthright or Fire Emblem Fates Conquest and would give access to the corresponding story path, with the other two being available to download for half the price of the base game.
The digital version worked differently, however. The first six chapters are the same for every story path, so the digital copy doesn't differentiate between story paths, and is just listed as Fire Emblem Fates. After finishing chapter 6, the player can download any one of the three paths they like, but are then locked out of the other story paths until they pay the standard fee. Essentially, all three paths are presented as DLC, but purchasing the game awards the player with a credit to get one of the paths for free.
While that method seems preferable for the most part, it's introduced a bit of an awkward situation with the eShop's upcoming closure. Someone could easily buy Fates a day or two before it closes and if they don't reach chapter 6 by March 27, they will be locked out of getting any additional path, leaving them paying full price for what is essentially a prologue. So, while Fates will be delisted from sale on February 28, the DLC routes will remain available until the eShop's closure, giving players extra time to reach chapter 6 and make their decision.
As of right now, it seems this will only be the case in the UK and Japan. The American release of Fates appears to have mirrored the structure of the physical release, and there is no notice of Fates being delisted early on the American website or any associated social media.