How to fix  missing icons and labels in System Preferences -> Spotlight?
Assuming your drive passes hardware verification, you might want to rebuild your spotlight index.

First though, repair permissions as much as possible.

Rebuilding the spotlight index is straightforward but time consuming. You will see that it is indexing as the spotlight magnifying glass icon will have a dot in the center of the glass.

This is how to reindex your drive:


Launch System Preferences from the  Apple menu
Click on “Spotlight” and then click on the “Privacy” tab
Drag Macintosh HD (and other drives if necessary) into this window





Click “OK” when asked to confirm
Now select the drive(s) you just added and click the “-” minus button to remove it from the list (weird right). Note: if an item is left under the “Privacy” list, it will exclude from Spotlight indexing completely.





Spotlight will immediately begin to reindex the drive(s) you added and then removed from the Privacy list. Note: How long it takes to reindex the drive varies, ranging from 30 minutes to several hours, depending on the speed of the drive and it’s contents. At any point, you can pull down the Spotlight menu and check the progress:





The Mac will probably feel sluggish during reindexing as the mdworker and mds processes run and consume a lot of CPU and cause a lot of disk activity.
After all this, if the problem still occurs, here are some other techniques:


Alternative #1: Kill SystemUIServer

Launch ‘Activity Monitor’ (located in /Applications/Utilities/).

Locate the process ‘SystemUIServer’, highlight it, and click the red button “Quit Process”.

Within a few seconds the menubar will rebuild itself and often Spotlight will magically work.

Alternative #2: Rebuild the Spotlight Index manually

Launch ‘Terminal’ (located in /Applications/Utilities/)
At the command prompt, type this exactly (copy and paste):
sudo mdutil -E /

You will be asked for your password, provide it, as this command requires administrator privileges to run.

You will receive a confirmation message saying that index will be rebuilt.

Wait until index is finished rebuilding, this can take a while depending on the size of your hard drive, amount of files, etc.

Alternative #3: Change Desktop Resolution

This is a strange fix but it works sometimes.

Open “System Preferences” via the Apple Menu

Click ‘Displays’ and select a resolution smaller than what you are currently using, 640×480 seems to always work

Select your native resolution again, changing your screen resolution back to normal

The Spotlight search tray will magically become available again

Alternative #4: Clear caches and preferences

Clear caches and preferences relating to Spotlight, this is best done using a tool like OnyX, MainMenu and/or Cocktail.

Alternative #5: Clean the Font caches

Sometimes, this is adequate to repair a screwy Spotlight, but it won’t hurt to clear them all

Hope this helps (I got this information from experience, but a lot of the text is lifted from OSXDaily.)