I have been having the same issue on my MacBook Pro 2017. I have been able to temporarily fix this issue but don't shut down the laptop or you will have to redo these steps. I expect apple to come out with an update soon.
Step 1: Open terminal (Finder -> Applications -> Utilities) and type the following command to erase and rebuild index:
sudo mdutil -E /
Step 2: Open activity monitor (Finder -> Applications -> Utilities)
Under CPU find "SystemUIServer"
Double click on this
Then click quit
The OS should restart the process and both messages and spotlight search should work
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This has helped me while my computer is on but if I shut down and restart the problem will show up again! Hope this helps.