In the past couple of months there have been a series of hacks that have utilised an exploit in the 3DS Web Browser; the New Nintendo 3DS has been excluded due to it having a different browser app. The exploit was used for multiple applications, such as loading Pokémon into the latest releases or even running emulated Game Boy Color ROMS on the portable. This browser-based hack also notably made the 3DS region-free, allowing cartridges from any region to run.
The most recent use of this browser exploit may have prompted action from Nintendo, however, as it bypassed the microtransactions in Pokémon Shuffle to make all items in the game's shop free, allowing users to pick up all the hearts and coins they desire. All of these uses for the browser exploit affected Nintendo, undoubtedly, but the Shuffle example would have cost - potentially - significant revenue if it had become widely used.
Today's very small system update to version 9.5.0-23 appears to have shut down this web browser exploit, which will have in turn locked out all of these hacks. We've had a look around some forums and it seems that this latest update's had no impact on the main flashcard services, so Nintendo evidently focused on shutting down the weakness in the web browser; as is typical of Nintendo updates it's required before access is granted to online services such as the eShop, making it a necessity for all but the most dedicated hackers. As mentioned above, this issue was never applicable on the New Nintendo 3DS.
Nintendo's certainly closed off - for now - a fairly substantial exploit that had been used for multiple purposes. Whether this was in the works for a while following revelations of the region-free or Game Boy Color ROM hacks, or whether it was rushed through in response to the Pokémon Shuffle exploit, it seems Nintendo's shut off another unauthorised loophole.
As per our policy we won't link to the forums where this exploit is being discussed, and ask that all discussion on the topic sticks to our - recently updated - Community Rules.