There is nothing wrong with accessing two databases from the same application. This is a commonly used model. It is not uncommon to have a Node server to access both Mongodb and Redis, using each for its own strengths. You just need to link the data relationships in the application, not in the database.
Node is particularly suitable for applications with multiple databases, as you can access multiple resources at the same time. The async package makes it easy to query multiple databases at once and combine the results. This is what synchronous servers usually do in order, waiting for one result before sending a request for a second result. Therefore, if you take full advantage of Node's capabilities, you will have a better experience accessing multiple data sources, and then you can use many other popular web development platforms.