Are you going to be using Leupold rings and bases. According to their website:
"50mm OBJECTIVES will almost always use HIGH rings in a given style. In certain instances, such as with extremely heavy barrels or some makes of firearm, SUPER HIGH rings may be necessary."
So with a standard barrel, you should be good with high rings. It's possible that you could go with medium rings, but it really depends on the scope (i.e. casing thickness around the objective, ect.)
It won't cause any sighting issues past your zero range, however shooting at a distance shorter than your zero you will have to compensate for the bullets impact being a little lower than you would on a low or medium mounted 3-9x40.
Also, if their is a possibility of a close-ish moving shot (such as deer or coyote hunting) the 2.5-10x50 will be better because the lower zoom will give you a wider field of view and quicker target acquisition. Also at powers above x10, a good paralax adjustment is great to have, if you do not have it on your scope, slight mis-positioning of your eye in relationship to the scope will cause the cross hairs to appear several inches away from the target. This can be solved, or at least improved, with a good pad or stock with adjustable comb.