Spoke with the regional rep here in chicago the other day. Canon is quite aware of this issue, and this was not overlooked when building the camera. The 7D, 5DIII and 1Dx all have the black focus points when in AI SERVO.
What's new? In previous camera models, the focus points were built into the focus screen, but now they use a HUD technology which (right now) does not allow for the red light to go away when the shutter is clicked, this affecting the exposure, etc.
She wrote this, "Yes, the focus point thing is something that we've heard a lot. I know that the engineers are taking it very seriously but I haven't heard whether or not they will (or can) make a change that would improve it. They've been very responsive and open to suggestions in the last couple of years so I know that they're listening and talking about it."
Let's all hope they do come to a solution, or it will be a LONG 2-4 years until the next camera, and a ton of missed shots, and a ton of screaming while shooting.