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You can still write directly to the file, less syntax - more attractiveness.
MEAN ( MongoDB, Express.js, Angular.js, Node.js ), sort of, almost de facto. "Relatively small project" without specifics can imply very different approaches.
Each project is unique. Some project will need only one type of database (MySQL / Mongo), and some project can use two or even more databases at the same time.
Mongo is handy for unique data that is "stored" and rarely changes. For example: logs, collection of unique statistics, where each document has different properties. Especially if the data does not need to be linked to each other, although it is possible to link them, but this has its own characteristics.
MySQL is organized in such a way that you often need to link data. Here, the types and composition of data are determined in advance and controlled by the DBMS itself.
For nodejs it doesn't matter, but for you as a developer and for your project it depends on your skills and on the project itself. If in doubt - take MySQL - it will be easier with SQL, you can make a database in SQL without even understanding what a database is and it will work.
PS. There is a good library - sequelize.
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