I was just thinking about this because I remember reading somewhere that some shelties can develop an eye disorder similar to night blindness. Maybe you should take him to the vet and have his eyes checked.
Dogs also go through another fear period during adolescence so it could be this, esp if he was okay before. They can be scared by the strangest things so being scared of the dark isn't so unusual.
If it is a fear period what everyone suggested will still help. Just make positive associations and don't push him too much that he starts to stress.
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