I don't think you're seeing the pistons, but rather the tops of the intake valves. The intake runners and valves do get dirty. Cleaning them can make the car run better, but you have to be careful how you do it. If the valve is open and you knock bits of carbon off, they can fall inside the cylinder and get ground up by the edge of the piston and the rings. Obviously this can cause scratching and extra engine wear as the ground-up carbon acts as an abrasive.
Also, if you spray it with a liquid and the valve is open, the liquid will run down into the cylinder. This can cause hydrolock when you start the engine the first time after the cleaning.
So if you want to clean the area, only clean the runners if the intake valves are closed. Use the shop vac before and after, and limit the amount of of liquid if you use a cleaning solution. Do not use chlorinated brake cleaner or you risk a nerve gas treatment when you start your car. To clean the rest of the runners, turn the engine by hand until the valves are closed and repeat the process.