Justin,
We did think about optical encoders. The first discussion which I had about these was with Tom Riegel over breakfast before the viewing London Marathon several years ago. Normally these would be fitted onto an existing a rotating shaft which you wanted to measure. The problem with the bicycle wheel there is no rotating axle. One possibility might be to use some gear arrangement such has Tom has on his counters. In fact one might try to use Tom's gears and replace the mechanical Veeder Root unit with the shaft encoder.
In August 2011 Dougie Roxburgh was wondering about shaft encoders to feed the iOS measurement app UKCM which he was developing. In fact he pointed me to some optical encoders with a USB interface which could directly interface with a normal computer. I think these are probably the sort of device you are referring to.
I decided not to pursue standard optical encoders but continued with my approach which had been derived from my thoughts all those years ago of how to set up to count each spoke passing. As far as I know it was the now retired measurer, Jack Selby, back in the 1980s who first tried to use a photo electric device to count the passage of spokes. I am not sure how well it worked, but it never caught on. Of course the very first bicycle measuring in the early 1960s was done by John Jewell who used a mechanical whole rev counter supplemented by manual spoke coke counting for the fractions of a revolution. That method is analogous to that developed by Neville Wood with the cheap cyclocomputers.
My bike is still in the workshop having the new front fork fitted. They are able to buy a suitable wheel for me rather than having to build one up. It is the particular mechanical fitting arrangements for the sensor which means I have to change the wheel and fork- rather a disadvantage, but then even the mechanical Jones Counter does not fit absolutely every bike.