Yes, some people naturally have better 3d spatial awareness. You can also train your eyes to be better over time. I work in orthotics and prosthetics and have to sculpt positive models of different body parts. We also have to do GAIT analysis where we have to observe the angle of different joints while a patient ambulates.

Some people are just better at it than others starting out, especially if they have prior similar experience. I teach a lot of residents and have noticed that students that have a background in art or construction tend to have a better eye for angles. A lot of it is just practicing by observing different angles compared to something that is known to be square.

I have also trained people who never seem to be able to improve their ability to see angles, which is a big hindrance in their careers. A lot of schools actually have students take a spacial awareness test before students begin studying in the field.