Probably a good part of the JS code is in the CLI app, which hasn't been updated much. Critical parts of the app are now in TypeScript, including the synchronizer, database and encryption service. Joplin Server is also entirely in TypeScript. Even the database rows are now typed thanks to sql-ts.
So anyway TypeScript has been a big win for the project as it made it possible to refactor and modernise many parts of it in a safe way, and make the code future proof and easier to work with! I expect we should get to over 50% over the next few months.