The retr0brite method only affects the surface of the brick and does not affect the clutch power.
I have used the method on several printed bricks. I have noticed the black printing will start to fade if the bricks are left in the solution for a long time. I have not noticed that it affects other colors as much as black, but this may be because the fading of black ink on a white or yellow background is more obvious. I have never seen the treatment completely erase any printing.
The length of time it takes the solution to start breaking down the ink is going to vary with the strength of the solution, the time in the solution and the amount of UV light. You can control the first two variables, but if you are using sunlight to provide the UV it is difficult to gauge or control.
The easiest variable to control is time. I would leave the bricks in the solution for perhaps an hour at a time, then take them out, rinse them off in water and dry them. Keep one of the yellowed bricks as a "control" against which you can compare the treated brick to get an idea of how much color has changed. Repeat as necessary until the brick is back to the color you want or you notice the ink beginning to fade.
Check the color of the bricks indoors. I use the sun on my front porch to provide the UV light when I'm soaking bricks, and I have noticed that bricks that look nice and white when I'm out in the bright sun will still appear yellowed when I get them inside.