Hide:
sudo chmod 600 /System/Library/CoreServices/Search.bundle/Contents/MacOS/Search
killall SystemUIServer
Show it again:
sudo chmod 755 /System/Library/CoreServices/Search.bundle/Contents/MacOS/Search
killall SystemUIServer
To disable spotlight only instead, without removing it from the top menu:
sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist
To enable it again:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist