Does LED matrix scanning reduce overall brightness?
Yes, if the LED current remains the same, then scanning will reduce the duty cycle and the amount of light.

You can offset this by increasing the LED current.  But, you need to watch out for the LED current ratings (continuous and pulsed), of course.

edit:
As an aside, keep in mind that human perception of the brightness is a nonlinear function of light output.

 (from here)