There shouldn't be any great confusion here.
How our eyes perceive the brightness of the LED as the average voltage?
Our eyes don't detect variations in light intensity above about 30 to 50 Hz very well. If they did we would have been driven mad by AC powered lighting and TV/monitor flicker.
It should make sense that if you blink a light at full power and high frequency that the average light level will be proportional to the PWM pulse width.
Is a dc motor working as a low pass filter?
Yes. The mechanical inertia of a motor means it smooths out the bursts of acceleration and deceleration to provide a smooth motion. If you drop the PWM frequency low enough you will start to get vibration.
Do the eye's perception and dc motor voltage result in the same graphics?
DC motor and graphics? You'll need to explain more.
What about a resistor working as a low pass filter or is it something else?
No, the eyes and the motor provide the low-pass filtering.
Similarly with the motor, the average motor current will vary with the PWM pulse width.