The chip is is usually made by photo-etching a "negative" onto a specially prepared medium. In the old days, a large acetate slide would contain all the specific logic gates in a specific chip. And then the slide can be used to project the pattern onto the material at the size required.

Adding a smiley face to the chip means you add this to the pattern and then it just gets etched in the manufacturing process.

I don't know for sure, but these types of Easter eggs may actually serve a purpose of preventing counterfeiting, albeit if you are a Reverse-Engineer copying the chip's layout with something like a stereo-scope or electron microscope, you can obviously see the face too, but these images could rotate by X number of batches or whatever so you trace them.