Is there a reason you’re not looking at tools explicitly built for this like orgmode, obsidian, task-warrior, etc? There’s a plethora of these tools and my experience with this is you really don’t want to over-engineer your productivity suite.
That said, if you go the SQL route, sqlite is the way to go. Other SQL databases must be run as a daemon whereas sqlite operates on a local file directly.
However any SQL database isnt going to have the CLI youre asking for. Its interface is… SQL, so you’re scripts are going to have a bunch of SQL code embedded that isnt easily reusable. A non-sql database will probably be better. I’m not familiar with them but I think there’s some that store their data as text files in a folder which is organized a certain way. But that starts looking like the tools I mentioned before.