Can you provide some examples of performance issues with the Aura, and I'll try looking at what's going on. (I can guarantee that I'll be able to pinpoint the problem, but I have just enough experience with Linux and its development tools that it should be a doable project.)

One thing that I can say is that a pure file system based solution wouldn't work in an ereader targeted at a general audience. Data such as the title, author, last position, etc. should be presented to those users rather than a list of directories and file names. Now that data has to be stored somewhere. While there are various ways to do this, a database is likely the most efficient means. Databases tend to be developed in such a way that searching, retrieving, storing, and removing data is done in an efficient manner. Using the data from the ebooks themselves would probably be the least efficient way to handle this, since it means opening and parsing data in multiple files when you want to present the data for a collection of books. (As added fun, some of that data may be compressed. Decompression adds even more overhead.)

There are other ways to handle it, such as a datafile per book (you're still accessing multiple files, but you can make the data more efficient to handle) or a datafile per directory (which really reduces to developing your own database, but it may be more efficient since it's application specific). Alas, many of those solutions make it much more difficult to add universal features such as searching your collection. That may not be an issue for you, but it almost certainly is an issue when the device has to reflect the needs of a general audience.

As for the tiles and sync hurting performance, I seriously hope not. Linux can certainly help background network operations without a noticeable impact on performance and the tiles shouldn't even be active in the background.