Technically the 36 hole rim would be stronger and it should go on the rear, the more aero wheel should be on the front anyways since the seat tube cuts most of the air that would hit the rear whereas the front has nothing to stop it. And the cross wind effect would be nil since the deep V probably isn't that substantial. There has been some experiments done that with certain cross winds a deep V rim can act like a sail and actually help you not hinder you, but I think the test was done on very deep rims.