We use Mongoose to access the DB.
I quote the purpose of Mongoose from their docs: "Mongoose provides a straight-forward, schema-based solution to model your application data. It includes built-in type casting, validation, query building, business logic hooks and more, out of the box."
Using the native mongo driver is basically the same thing as accessing the DB directly, which is obviously risky not just for a big project, but any project. That being said, we do use mongodb driver for quick DB migrations.