SQLite won't stop working but your format is proprietary. A markdown can be understood even without rendering to HTML but your tables are useless for an user without your app.
As far as I can tell, the whole app is open source (AGPL), and sqlite is obviously open source as well. I agree that markdown is more portable, but this setup is far from proprietary.
I may not have made the same decision (I love having my notes in markdown), but I think OP was quite thoughtful about it and has made an informed and reasonable decision.
I also use RTFD in the same application. This is a variant of RTF which can have embedded images. It's not universally supported like RTF, but there are sufficient third-party editors to leave me confident that I will be able to get at the information. This is for my 5-year files.