My understanding is as follows (my apologies if I am wrong!):
SQLite itself provides no encyption.
As an option, users can purchase a cryto module for $2000 from Dr Hipp's company http://www.hwaci.com/sw/sqlite/see.html. This provides a robust security system to those users that hooks into SQLite, but those users are not allowed to redistribute this system (understandably). This is based on AES encryption.
System.Data.SQLite uses the built in "hooks" to implement a custom "lower grade" security system based upon Microsoft Crypto-API / RC4: http://sqlite.phxsoftware.com/forums/p/473/2005.aspx#2005. In my opinion this provides excellent security for distributable databases on windows. However, it is obviously not compatible with AES!
I am not sure what SQLite Maestro uses - if self contained then it may use Dr Hipp's Crypto Module. If not, then it is most likely another custom encryption scheme. You can use it with other products that support the same scheme only.
In summary: use SQLite Maestro to read SQLite Maestro encrypted files. Use System.Data.SQLite to read System.Data.SQLite encrypted files**.
** There is an exception here: dhSQLite (for VB6) uses the same encryption scheme as System.Data.SQLite and I have found it to be compatible. This means that I can generate files with System.Data.SQLite and then read them in VB6 programs (and vice versa).