Humans are not mostly skin but that's most of what we can see of each other. It's a thin covering over the rest of the stuff that makes us human or what makes us who we are. so if something is only "skin-deep" that means that it only covers the surface of a much deeper truth about someone. They say "beauty is only skin deep" which would mean that just because someone looks beautiful on the outside doesn't mean they're not ugly on the inside (their personality) - so when we say something is "skin deep" what we mean is that it's a quality that would be a poor judge of overall character of a person.

If you look at an apple, skin can be shiny and bright without a mark, but you don't know how nice it tastes until you get past that nice exterior. It's the same with people. We all have a way that we want the world to see us, smart, attractive, kind, and so on. Once you get past that layer, there is a lot more to a person, like they have hobbies that they wouldn't talk about unless they were friends with you, or they have worries that they are dealing with. If you only know the surface stuff, you only know them in a superficial way, and it is not a very deep understanding, like the thickness of skin.

It means not deep at all, only what you can see. So it meams that there is nothing more to understand than what you can see with your eyes.