Have you saved them on your memory card?
If you have not, I am really sorry that your messages are gone.
If you have saved them on you memory card, you could download a recovery tool to help you. I know a free recovery tool: http://blog4mark.blogspot.com/2012/12/samsung-phone-rec...
What that means is that the information is removed from the directory. It has nothing to do with spotlight the iPhone has no idea that it exists. It's just like on a computer. Even though it's really there the computer thinks it isn't. The iPhone thinks it isn't there. It has nothing to do with how Spotlight works.