Couldn't they hire someone who actually has a *beep* facial deformity

They would have to find a child ACTOR with a facial deformity...not just anyone.

And that kid Jacob Tremblay can act.

They've used people who IRL were missing limbs to cover such characters, but AFAIK, those were only for short roles, and not thje entire movie. Here, that kid was a very large part of the movie.