Can I paint iPhone X earpiece speaker with permanent marker

There are cameras and sensors around the earpiece, so using a black marker could cover one of those and render it disabled.

It's your phone, so you can do whatever you want to it, including damaging it, which you could certainly do by using a magic marker on it. Also, don't plan on taking advantage of the warranty on your phone if you do. Didn't you put your $1,000 phone in a good protective case when you got it? It's never too late to put your phone in a case.