They're not reading every 2nd or 3rd pixel, that's for sure - if they were, they'd produce horrible moire and other artifacts.
Line-skipping was used in highly praised "still image cameras used for video", such as the 5Dmk2. And yes, that camera had lots of artifacts.
No idea about sources. I don't look for them when it's both self-evident and consistent with what Canon has done in the past.
If we are in the "speculation and hand-waving" department, I'd offer mine as well:
The 5Ds is clearly pitched at the stills photographer. Canon will have a video oriented 6D/5Dmk3 replacement soon. I would not expect the 5Ds to be particularly adept (for its price or introduction date) when it comes to video.
So do you have any other examples supporting your claim that "current 42MP and 50MP sensors can sample video at 25 or 50fps, utilising every pixel on the sensor"?
Am I right that the Sony A7rII does line-skipping in FF mode (strange wording in the link below), while the cropped "super 35" (18MP crop of 42MP) is 4k@25fps? Why would the worlds best camera sensor manufacturer do such a thing unless it is somewhat hard to read out all those pixels many times a second? If the camera can actually process and compress 100mbps lossy 4k@25p video, why use anything less than the optimal starting-point (42MP of full sensor area/resolution, properly downsampled to 4k)?
http://www.bhphotovideo.com/explora/video/hands-review/sony-a7rII"The camera also runs very hot when shooting 4K internally, to the point where overheating could be an issue in certain environments or shooting styles.
...
The full-frame mode uses the whole resolution of the sensor and thus uses pixel binning to down-sample it to 4K. While full frame isn’t quite as sharp as Super 35 and can pick up a small amount of moiré and aliasing in some shots,
"
-h