I don't know of any way to vary the intensity using only KeyShot animation.
You would need to render a "clown" pass of your animation where the LED is a unique flat color. Then in a program like Adobe After Effects this LED mask gets selected and you keyframe the intensity of the render layer.
Or as suggested below, you could do it the hard way. Render out individual frames including a clown pass, then in Photoshop select the LED and change the intensity frame-by-frame. It would be very hard to get a smooth result using this method.
Or, (I just thought of this) if the LED is behind a panel, create a disk with a curved slot cut-out and animate the disk to rotate between the LED and the panel. Presto! Pulsating LED.
Ed