I've recently switched to SilverBullet[1] as my day-to-day note taking and task tracking app, because of it's very powerful ability to embed little queries and scripts directly in a page to build lists/tables/links that based on data from other pages. This looks like an interesting way to leverage markdown libraries in different ways. Nice!
Astro does this by design as part of its content collections: https://docs.astro.build/en/guides/content-collections/
Since this presupposes Markdown of the flavor that comes with YAML frontmatter, and that frontmatter is doing all of the heavy lifting, this is more like a YAML database than a "Markdown database".
In any case, nowhere is it indicated why this approach (no matter what you call it) should be preferred over e.g. recfiles.
Notenik does has something like this: https://notenik.app/kb/app-overview.html