Typically, these third-party shops function as databases. They contain "tickets"—small files that tell the 3DS operating system that a user has the right to play a specific game. In the modding scene, this is often tied to the installation of CIAs (CTR Importable Archives).
Let’s kill the mystery immediately. The Ghost eShop is not a secret server run by Nintendo employees in the afterlife. It is also not a resurgence of the official Network. Nintendo 3ds Ghost Eshop
The Ghost eShop is not on the official Universal Updater (usually). You will need to find the latest .cia release from the developer's GitHub or a trusted forum like GBAtemp. Typically, these third-party shops function as databases