The .NET provider uses RC4 encryption. The entire file is encrypted, including the metadata. SQLite the engine may store unencrypted pages in its internal cache, but I don't really know for sure.
The bottom line is that nothing is safe from a hacker who has your binaries and database on his/her computer and is determined to read your data.
It is impossible to design an unhackable program that is designed to run on a local computer. Anytime a hacker has access to a debugger and locally-running code, you are vulnerable in some fashion or another.