You can use a custom post-processing shader to crop the black borders:
(based on Derek's code for Resident Evil 4)
Just put it in Dolphin/Shaders/zoom.glsl and enable it.
Code:
void main() {
float2 coords = GetCoordinates() - float2(0.5, 0.5);
float2 new_coords = float2(coords.x, coords.y*0.86);
float2 sample_coords = new_coords + float2(0.5, 0.5);
SetOutput(SampleLocation(sample_coords));
}
Just put it in Dolphin/Shaders/zoom.glsl and enable it.