My information is dated but years ago I asked a similar question.The research found that the use of panniers on the front wheel was best for aerodynamics and handling.I bought some Blackburn panniers for the F wheel and have been pleased with them.
With the two choices you have presented I would choose
#1 also as your body will block most of the wind.If aerodynamics is important to you the use of a small bubble windscreen will help more than anything.