When you delete your sms, and it still show up in spotlight when you search for it, because it is saved in a different file, not your sms.db! And that file is SMSSearchdb.sqlitedb located in

var/mobile/library/spotlight/com.apple.MobileSMS/SMSSearchdb.sqlitedb

This file stored all the deleted text as well as none-deleted text messages. It also stores contact names. If search for number doesnt show all the text messages, try search for contact names instead!

To read deleted sms in these files, you have to read by a simple text edit program, NOT any sqlite database reader, bc it wont show the flagged deleted sms! The order of the sms in there when reading by a text edit program is kinda mixed up a bit!

If you want to really clear your sms deleted history, probably just delete the whole file! Do it at your own risk!