The docs do not show any details on how their object storage engine works. The API is pretty simple. It isn't hard to provide a very robust storage engine that provides such an API. Their FAQ (I think) however does state that they have been running for about a year and have never lost any data; if that means anything ;).
I would think that if appjet were to gain significant traction, you would need integration into other persistent options such as MySQL and Postgres. The easiest thing (I'm guessing) would be to just write simple js wrappers to an existing Java based ORM.
Wow, I sure am answering a lot of questions about appjet considering I just discovered it a few hours ago!!!