Over the long term you expect the weather to average out and cancel itself out of the calculation. The question is does the headwind lower your efficiency more than the equivalent tailwind raise your efficiency?
Yes, in general getting 50/50 up+down hills, as tail+head winds decrease your total efficiency, as if you drive both directions (getting both the advantage and disadvantage), then you tend to drive the disadvantaged half slower (but not using less power, so no efficiency benefits from that) = it affects you longer = it has more effect on efficiency.