Uniform values are not updated from those properties:

ShaderEffect 
{
   property var v1: Qt.vector2d(1.0,1.0)
   property var q1: Qt.quaternion(1.0,1.0)
   property vector2d v2: Qt.vector2d(1.0,1.0)
   property quaternion q2: Qt.quaternion(1.0,1.0)

   fragmentShader: "
        uniform vec2 v1;
        uniform vec2 v2;
        uniform vec4 q1;
        uniform vec4 q2;
   ...

This behavior is really confusing because QVector3D, QVector4D, QMatrix4x4 are handled.

Quick look into code, and I figure out changes need inside_QQuickCustomMaterialShader::updateState_ method.
Values QMetaType::QVector2D and QMetaType::QQuaternion should be in switch statement. Default should also rise an error in log, so it will not confuse when using wrong type.