Is there an API for any version of Windows Phone that allows an application to sniff incoming SMS messages and transparently send ones, replacing the built-in SMS application with one that supports encryption like an Android's SMSSecure does?
You can't override basic apps on Windows Phone. You can't modify Contacts, Photos, Messages, Calendar...
If you want to send a SMS message you can use these lines of code:
Windows.ApplicationModel.Chat.ChatMessage msg = new Windows.ApplicationModel.Chat.ChatMessage();
msg.Body = "Hello d33tah. Nice to see you on stackoverflow!";
msg.Recipients.Add("10086");
msg.Recipients.Add("10010");
await Windows.ApplicationModel.Chat.ChatMessageManager.ShowComposeSmsMessageAsync(msg);
You can read this article in order to get more information.