As of March 27, 2023, Nintendo has officially closed the Nintendo 3DS eShop. While it is still possible to redownload purchased games, new purchases are impossible. Consequently, The Binding of Isaac: Rebirth can no longer be purchased legally through official channels on the 3DS hardware.
If you are looking for information regarding the game's existence and technical state on the 3DS, these resources cover the major milestones: The Initial Ban (2012): Early articles from Nintendo World Report isaac 3ds rom
