Thanks for your feedback!
We're currently working on an export plugin system that will likely make it into the next release; this will include the missing data (specifically, notes in a plain text and an HTML rendition) in the JSON-LD export, too.
That said, I would like to emphasise that you need not worry about lock-in of your data with Tropy. Tropy itself is free and open source and the project files are SQLite databases. We will continue to improve the JSON-LD export and add a number of plugins to export directly to other software such as Omeka, but it is also possible to access your data directly with SQLite. The database schema is not trivial but it's definitely possible to access your data with SQL completely without the use of Tropy itself.