Unfortunately, no, for APIs you can have a single bootstrap.js file located in ./config/functions/bootstrap.js.
But you can have an individual bootstrap.js file per Plugin ./plugins/{plugin-name}/config/functions/bootstrap.js. In that case, you can create a plugin called “Shop” and create multiple APIs inside it like Orders, Products, Clients, etc. But the problem that I noticed when using plugins CLI is that it doesn’t auto-populate the routes.json file with the newly created API. So you must define all the routes manually 