Vertical targeting compensates elevation for drop. If you disable it your guns simply shoot parallel to your plane and you must compensate for drop yourself (especially when shooting at targets quite a distance away). If enabled your guns and gunsight will be aligned such that your guns pass through your aimpoint at your set gun distance. When shooting at other distances you must correct for this yourself.
Essential on planes with several types of guns loaded. Makes sure your MGs and Cannons hit at the same point instead of letting them drop at their separate arcs.