I have received a Notice of Intended Prosecution for crossing a red traffic light. The NIP states that the time into red was only 1 second. The amber light was previously on for 2.9 seconds. Legally does the NIP apply if the red light was only illuminated for a second? Is it worth appealing?

Red traffic light offences are strict liability.  The rules are that you must stop on amber, unless it is unsafe to do so. You must stop on red, regardless of the circumstances.  If the lights were red for one second, you will be convicted. You can ask to see the photographic evidence etc, but if the lights were red when any part of your vehicle crossed the stop line, you will lose.
 
You may therefore be better off taking the 3 points and £60 fine as that offer will be withdrawn if you proceed to Court.