ECS is useful for real-time, but it means that you are rolling your own query logic. This is fine for the runtime of game engines because they generally aren't dealing with that many data types(for the very most complex AAA games, perhaps a few hundred components) and the queries used at runtime are simple and tend to demand optimization at the data structure level.
If your purpose is an editing tool you may want to reconsider. Editing changes the goal in a very substantial way and the complexity of your queries goes way up, which is where SQL syntax absolutely shines.
That conflates the use of the schema with the use of the format features. You can, in fact, use your custom in-memory structures and then "slurp it out" to BLOB when you're ready to save.
Data mining is an old gamedev worry. Nobody who's been doing it for a while particularly cares. If the game is remotely popular, data mining will happen. Disassembly to find the decrypt function is a talent possessed by many, many people who have the reverse-engineering bug. If you then obfuscate the code, you have made things interesting and then increasingly talented people will try to have a go at it. If you combine a changing obfuscating technique with updates, you can slow down community possession of the game with respect to modding etc., and Minecraft worked that way in its beta phases. But it's really all a question of your purpose at that point.
If your purpose is an editing tool you may want to reconsider. Editing changes the goal in a very substantial way and the complexity of your queries goes way up, which is where SQL syntax absolutely shines.