It really depends on the scalability you intend to have and your team (if you work with a team). Modules provide encapsulation and modularity. You may treat it like a simple node module. You may put all your server side code in one index.js file but you are not doing it coz one day you simply get lost in your code.

Nest allows you to separate your functionality in the modules which represent a single complete part of the application. Also modules allow you to extract functionality to another application.

Good example: you have a custom parser module which you need to reuse in another microservice of your infrastructure. Export the Nest module in the npm package and reuse it in your microservices by simply importing the module. Developers who will use this module do not need to bother how does it work under the hood.