Does empennage height above the main wing matter
The critical aspect for Vertical stab height is its rolling torque and how it affects the balance of total side slip forces on the aircraft, including wing, fuselage, landing gear, engine mounts.

As viewed from the side, for the same area, a higher aspect Vertical stab will create more rolling torque and be structurally weaker than a more square design.  

More important is Vertical stab area, your weather vane, which affects directional stability and spiral stability.  Very important to get this right.  Adequate area is needed to avoid "Dutch Rolling".  Note that a high wing design needs less dihedral, there for can have a smaller Vertical stab.

Also, the tractor propulsion design, with the CG (and wing)  set as far forward as possible, also lowers the Vertical stab and Horizontal stab area requirement, resulting in significant reduction of drag.

But, unless extreme performance is needed, it is best to slightly overdesign the empennage and play it safe.  Study of existing designs past and present will be of great help.