I have a bit of conceptual question regarding the structure of users and their documents.
Is it a good practice to give each user within CouchDB their own databa
The solution is as old as web applications - if you think of a mySQL database there is nothing in the database to stop user B viewing records belonging to user A - it is all coded in the application layer.
In CouchDB there is likewise no completely secure way to prevent user B from accessing documents written by user A. You would need to code this in your application layer just as before.
Provided you have a web application between CouchDB and the users you have no problem. The issue comes when you allow CouchDB to serve requests directly.