If I uninstall the app, is my data gone?

Uninstalling removes the app itself. The app's private data folder (the database, encrypted note cache, sealed credentials) and the Keychain entries may linger until removed — but the encrypted cache is unreadable without the Keychain key. Your saved PDFs in ~/Documents/Supernote are your own files and stay put. Anything that lives in the Supernote cloud, on your device, or in a connected to-do app is unaffected by uninstalling this app.