Do manual shades count as glare control devices?

yes

Even though the credit lists manual shading devices as being appropriate forms of glare control. The simulation method specifies that automated glare control devices are the only way to exclude the maximum number of foot-candles on a simulation based calculation. If manual shading devices are acceptable, how can you count them when taking a simulation approach for credit compliance?

You can't. Well you can simulate blinds, but the requirements for simulation as of now is based on that you can't count on the occupants raising and lowering the blinds to control the glare aspect. They must be there so that they can control the glare, but you can;t demonstrate credit compliance with them in your simulation. That is why 2012 has brought in the spatial daylight autonomy metric into play. Automatic blinds eliminates the unpredictable nature of people. So the blinds will go up when they can, therefore allowing daylight in and hopefully the lights dimming down or off. Credit was written as best as possible to address the major issues found in day lighting without making it complicated or economically unfeasible to document the credit.