I've never heard of anyone cleaning the AF sensor, dust on it does not show in the images, and is very unlikely to affect exposure, so the risk versus improvement ratio is pretty high. Same for the sub mirror.
Marsu42 was referring to the AF accuracy.
@ marsu42; you have to raise the mirror to expose the AF module, so I have to do it as per the camera sensor cleaning operation.
Agreed you are blowing dust from one place to another, but on a number of occasions I have had an outer point that seems to have failed altogether. I give the AF module and sensor a good blow with a rocket blower and that outer point that seems to have failed works fine again.
Remember that with zoom lenses that alter their physical length such as the 24-105, 24-70, 70-300, 100-400 etc, their zoom action is constantly pumping air in and out of the camera. Although the weather sealed lenses do have a brush 'seal' around the inner barrel it sure as hell aint a good dust seal after a fair amount of use. So someone who uses these types of lenses a lot are going to get more dust issues than someone who just uses primes, even though they may be changing lenses more.
A tip for you on focusing on 'naked' horses - I am presuming you are shooting wild ones without any head collars or tack on - try using Servo AF with the centre points expanded, and unless very close have all AF points activated. I know this sounds contrary to 'single shot AF' and centre point being more accurate, but I have found that when trying to focus an an animal with very flat fur such as a horse, the aformentioned method is much more successful with the 5DII and 6D.