At its core, a "WhatsApp Shell" is a bot. It is a piece of software running on a server that connects to the WhatsApp network via the WhatsApp Business API (or, more commonly in the hobbyist space, through unofficial libraries like whatsapp-web.js or Baileys ).
In security research and CTF (Capture The Flag) scenarios, "WhatsApp Shell" can refer to a that uses WhatsApp as the communication channel. whatsapp shell