Depends on what is more important to you - speed or security.
Speed
Definitely SQLite, it isn't exactly the cleanest, but definitely the fastest way.
Security
Custom files which are encrypted - it will take a while to read the whole file and then decrypt it in order to display it, but you can be sure that the attacker will access the files encrypted and without the knowledge of the encryption - those data would be useless to him.
EPUB
If you're concerned about security then don't, unless you know how to apply DRM...and that is not a way to go honestly.