You are getting the error due to running 32-bit AutoIt. It needs to be run in as 64-bit. Add the following to the top of your script, and it will work, at least for me it does.
#AutoIt3Wrapper_UseX64=Y ;(Y/N) Use AutoIt3_x64 or Aut2Exe_x64. Default=N
#include <SQLite.au3>
#include <SQLite.dll.au3>
_SQLite_Startup(@ScriptDir & "\Config\sqlite3_x64.dll", False, 1)
If @error Then
MsgBox(16, "SQLite Error", "SQLite3.dll Can't be Loaded! - " & $__g_hPrintCallback_SQLite & @CRLF & @CRLF & "Exiting application / Zavolej Honzovi")
Exit -1
EndIf
Adam