The fact that he is a robot is not important.

• Close friends and family members do not use くん/さん at all when they call one another.
• At classrooms, English-based names may resist くん/さん earlier because everyone knows it's not used outside Japan.
• Generally, mass media do not use くん/さん to address a celebrity, active sport player, etc (there are complicated house rules). Ordinary people do not use くん/さん when they refer to them. I have never thought of calling Super Man スーパーマンさん even though he is not a robot.

アトムくん is a perfectly valid option for someone who works with Atom in a businesslike manner, like his teacher.

The fact that he is a robot is not important.

• Close friends and family members do not use くん/さん at all when they call one another.
• At classrooms, English-based names may resist くん/さん earlier because everyone knows it's not used outside Japan.
• Generally, mass media do not use くん/さん to address a celebrity, active sport player, etc (there are complicated house rules). Ordinary people do not use くん/さん when they refer to them.

アトムくん is a perfectly valid option to those who work with Atom in a businesslike manner, like his teacher.