I agree with David, that nadir images are mainly taken in order to generate orthomosaics.
In general, your model will have altitudes of any point that is visible on the input images. If, for example, the wall of a building is visible on the input images (at least 2 images), then this point will be reconstructed in 3D (you will take X,Y,Z coordinates). If the wall of a building is not visible, then it is impossible to be reconstructed in 3D.
So, if your images have only the roof, you should expect the altitude for the roof. If you want the altitude of the walls, you should fly in oblique mode (tilt your camera).
Flying higher you will capture more the facades. You could do the same flying lower, but increasing the image rate.
I hope it helps,