Ground clearance does have some effect on the air resistance, as it minimizes the drag due to crosswinds below the coach, especially when the wind is coming at an angle to the train. In these cases, a train with a lower ground clearance will show more regular face to the oncoming wind and the flow around the coach will be more streamlined than the one with a higher ground clearance ( with other uncovered equipment hanging below the coach).
Air resistance is usually dependent on the cross-sectional area of the train. A low-floored coach will have a smaller cross section and hence lower air resistance. Usually, below 80kmph, the cross sectional area does not have a significant effect on the...
more... air resistance, but above 80kmph, it does have a significant effect. This is why high speed train-sets are either short in height, or using an envelope around the undersides of the coach and mimic a lower ground clearance.