I don't see Night Shift after upgrading to IOS 9.3. I was using beta 9.3, but deleted the profile after I didn't see Night Shift in Display & Brightness after upgrading
Is there something I am missing? Using Ipod Touch 5th Gen.
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Night shift isn't supported on your hardware. See the footnote 1:
Night Shift is available on iPhone 5s or later, iPad Pro, iPad Air or later, iPad mini 2 or later, and iPod touch (6th generation)
Have you tried to reset the settings (don't reset the whole data, just general settings). I hope this will help you fix the issue. Can you enable the feature from the Settings app or is it even missing from there too?
Update: Night Shift isn't supportive for your version. More info from here