Thinking about this more - this might be a perfect use case for Redbean. Backend mini-app user data could be stored in SQLite. The server could store the actual apps' static files in its internal zip archive. All of that could easily be managed with a sprinkling of Lua.

The mini-apps could store data in localStorage, but that would expose the data to other mini-apps. Maybe build an easy API that functions nearly equivalently against a Lua endpoint.