I'm sure plenty will disagree, but hand sharpening is faster, cheaper and more consistant than using a machine. The real reason may be that they already have old belt grinder and buffer stand setups for polishing, etc in a lot of these factories and they need to use them for something.
I've been in the Benchmade, Kershaw, and Gerber factories and spoken with engineers in each of these factories about why they haven't automated sharpening. The short answer is that the ROI is much longer than 5 years and the resulting blade isn't significantly better than a hand sharpened blade. Based on the information I've collected the processes that shape the blade before it can be sharpened are not repeatable enough to make fully automated sharpening possible, you'd end up with off center edges, inconsistant edge bevels and poorly sharpened blades. Leatherman uses a robot to sharpen some of their blades and their edge consistancy and sharpness are worse than the blades that are sharpened by hand.
The edge pro, wicked edge, and other guided sharpening systems are not nearly efficient enough for high volume production work, especially for setting the bevel on a factory un-sharpened blade, automating a system like the edge pro isn't as simple as hooking it up to a pneumatic cylinder or servo drive. When you use a guided system you are still using human tactile feedback and human response, which is difficult to reproduce electro-mechanically, even in 2013.