Is there any purpose of disallowing AF when the lens aperture become smaller than f/5.6 with the usage of extender ? By taping the contacts of the extender to allow AF, will it cause any problems or damage to the lens ?
Don't it is a "allow" verses "disallow" thing. Just that the AF module requires certain minimum amount of light to work properly and if you have a small maximum aperture it may not work most of the time. Just my thought.
As Ansel have said, it's not a matter of allow or disallowing. AF sensors fare badly in scenes with low contrast and lowlight situations. Now suppose you stop down your lens using the DOF preview button from f2.8 to f5.6. The picture you see in the viewfinder becomes quite a bit darker. It's due to this which causes the camera to stop AF. If I'm not wrong, f8 is the boundary where most cameras stop being able to AF. f5.6 is still possible.