The random removal of the DSiWare games came to the surprise of many, including those involved in the making of some of those games, such as Shantae creator Matt Bozon. However, again, seemingly out of nowhere, it's looking like some of the removed DSiWare games have actually made its way back onto the 3DS eShop.
3DS owners noticed last night that for one reason or another, almost all of the removed DSiWare titles returned to the eShop just as silently and swiftly as they were taken away earlier this week. This includes the return of some popular titles such as Nintendo's Art Academy series, Plants vs. Zombies, and most notably, Shantae: Risky's Revenge.
The return of the missing DSiWare games was reported by Delisted Games, a database made to chronicle information on discontinued video games. Strangely enough, while many of the bigger DSiWare titles reappeared on the 3DS eShop at the same time, it seems that there were some stragglers. Initially, some games from the Petz series didn't return to the eShop until later, and some other DSiWare like Digger Dan & Kaboom and Match Up! have yet to return to the digital shop. At the time of this writing, Nintendo still has yet to comment on these occurrences.
While it's not known what exactly is going on with the 3DS eShop, many speculate that the removal of the games was largely unintentional and due to something like a change in servers. Although the 3DS has been discontinued for a few months, hopefully fans will receive a proper notice ahead of time should Nintendo decide to officially delist any DSiWare titles in the future.
Source: Delisted Games