Ok, so i stuck one of my disks under the microscope and to be honest they look pretty darn good! The toner is solid and the edges are a little 'furry' but only about 1 micron (1/1000mm) is furry. I doubt many commercial encoders would be much better.

There were a couple of sub micron holes but this particular disk had not been cared for - it was one of my test ones. I doubt they would have any effect anyway.

So, where does that leave me? Well, it means doubling the disks is probably pointless but making the clear slots smaller might be of some help. I sincerely doubt that a 1 micron 'edge' is going to cause a problem for a sensor that is likely to have a beam width of probably at least 10 times that.