Running CorFlags.exe against System.Data.SQLite.dll from http://sqlite.phxsoftware.com/ produces the following output.
Version : v2.0.50727
CL
If you download the SQLite-1.0.66.0-binaries.zip file from sourceforget.net then this contains a bin/x64 directory with a System.Data.SQLite.dll file which is what you are looking for.
It also has an Itanium directory too..
The URL is:
http://sourceforge.net/projects/sqlite-dotnet2/files/SQLite%20for%20ADO.NET%202.0/1.0.66.0/