I recently connected my new MacBook to my iMac with the MacBook in target disk mode and switched off Spotlight on the mounted disk (i.e. the MacBook's hard drive) via the System Preferences -> Spotlight -> Privacy panel.
It turns out this disables Spotlight for that drive on the MacBook, even when it is booted up normally and is no longer being used as a FireWire drive. It then has to be enabled again (and the index recreated) in the System Preferences on the computer that was used in target disk mode.
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