That seems like a configuration error or a bug. I currently have eight external USB drives indexed through Spotlight on 10.9 without issues.

Check the Spotlight settings to make sure your drives are not excluded, and trigger a full reindexing process through the Terminal.

Just go in the from the command line and delete the spotlight (V100 etc) files in their root.

Or add them in the "privacy" section of Spotlight preferences, and then remove them, to have the index rebuilt.

Downvotes for an issue-fix suggestion? Really?

In your spotlight settings, exclude the external drives from indexing and then add them again.