Your filesystem is very much not a database, and you risk data corruption and loss by using markdown files as a database, especially if you have multiple programs reading and writing to and from the same files. Things will start getting weird and you will start rebuilding an ACID compliant database engine in your application layer.
That said, I love markdown. It's great. Simple.
For applications requiring simultaneous writes from multiple programs (concurrency) or ACID transaction properties, using Markdown files as a substitute for a database is undoubtedly an anti-pattern and entails a risk of data corruption.
Strictly we could have titled this: the markdown database pattern for small personal databases.
The point was that for personal use e.g. keeping a list of projects, or books etc this is perfect. Or even for maintaining this list on a website.
It isn't for multiple simultaneous writes