I was having the same issue and what worked for me, without reseting my phone, was the following:
1. Go to <settings><general><spotlight search><uncheck messages>
2. Then turn your phone off and wait a minute! Turn your phone back on and off again 2 or 3 more times while waiting a minute inbetween turning it off!
3. After you are done doing that go back to step 1 and <check messages>!
4. Now go to your spotlight search and those messages should be deleted! If they are deleted I would recommend going back to step 1 and <uncheck messages> so you do not have the same problem with messages showing up again in the spotlight search!
It works for Mail too! Just follow the same steps listed above but uncheck mail instead of messages or do both at the same time!!
Here is an extra tip which will remove deleted Mail Messages, just follow the steps below:
1. Go to <settings><mail, contacts, calendars><your mail account> scroll down and click <advanced> Now click <remove> under the title Deleted Messages and you can choose to have your mail removed After One Day, After One Week, After One Month or Never.
I hope this reply was detailed enough and I really hope it works for you like it did for me! Good Luck!!!