Mr Hughes also faces two charges relating to indecent photographs of children. It is alleged he took indecent photos of a child and he is accused of having indecent photos of a child under 16 on 2 August.
Mr Hughes, who spoke only to confirm his name, address and date of birth, was remanded in custody until 9 August, but need not appear before the court again until 30 August.
A crowd of about 100 people had gathered outside the court by the time Mr Hughes arrived in a police car. People jeered and shouted "animal" and "beast". Some kicked the car.
Sophie disappeared early on Sunday morning from her uncle's garden in Llandudno where she was camping with her sister Jemma and cousin Luke, both nine. Her parents, Chris and Julie, of Great Budworth, Cheshire, have issued appeals for her killer to be found.
Mr Hughes was charged on Thursday night, shortly after reports that Sophie's nightdress had been found in undergrowth three-quarters of a mile from her uncle's garden.
The crowd had swollen to 350 by the time Mr Hughes left the court. Two riot vans and up to 40 police cleared a way for his removal.