Are there any benefits to using MongoDB for a Node.js application rather than a traditional SQL database such as MySQL, if I'm not planning to have large (>1000 item) collections and am already comfortable with SQL?
MongoDB is schema-less document based database. This means you can insert a JSON object with other nested objects. This can make development easier, especially for prototyping.
For a small project, why not? For a larger project you should do more research. Large or small, doesn't hurt to do the research anyway. You want to consider how your application uses the database (reads vs writes) and how MongoDB scales horizontally, and how it handles failures.
There's a thing called the CAP theorem that defines NoSQL databases. MongoDB is CP. This visual guide shows the relationships between different databases. What is most important to you and your application?
Something else to consider is that most NoSQL databases are not ACID compliant. If you're using MySQL with InnoDB, that can be something significant to give up, depending on your application. For example, transactions might be something you might not want to give up.
Lots of pros and cons. Best thing to ask yourself is: What am I gaining? What am I giving up? There are many things, and it really depends on your use-case.
There are lots of reasons to stick with a simple dbms for a small-scale application. One of them is the widespread availability of cheap hosting services providing MySQL. Another is ease of deployment and maintenance.
Of course, if you're trying to learn to use MongoDB, go for it!