Is there a way to read/write to a file or database using papyrus? I'd like to be able to store and retrieve information about the objects within an asset (like the list of weapons within a chest). I'd like to be able to manipulate these values from one or more scripts attached to different assets in the game. It would also need to be persistent in the sense that the values should be stored even when the user exits the game.

Or any recommendations on alternate methods? There is a mod out there that tracks what books have been read, and assigns a glow effect should they be new. I'm assuming the list of read books would have to be stored somewhere...

Papyrus doesn't support file I/O of any kind. The most you can do is print messages to the built-in debug log. Look into arrays and form lists for alternate methods of implementation.