Police discovered Shannon on Friday in the drawer of a sofa-bed at an apartment less than one mile from her home in Dewsbury, in northern England.
Michael Donovan, 39, formerly known as Paul Drake, was arrested on suspicion of abducting Shannon. He is the uncle of Shannon's stepfather, Craig Meehan.
"Shannon has had a comfortable and settled night and is starting on the road to recovery following her ordeal," a statement from West Yorkshire police said the day after she was found.
"She spent last night watching DVDs, has had breakfast this morning and has been playing with a kitten ... (and) she will continue to be supported by specially trained officers who will try to carefully establish what has happened since she went missing on February 19th.," the statement said. Although Shannon was briefly re-united with her mother, 32-year-old Karen Matthews, police have placed the girl in protective custody.
Officials said they still don't know what happened to her, including whether any one other than the arrested man could have also been involved in her kidnapping.
"We're getting mixed reports about how Shannon feels," Dr. Lesley Perman-Kerr, a psychologist and psychotherapist who works in private police and emergency services, told ABC News. "I'm assuming everything seems unreal for her. She is being reassured by spending time with the police team but she'll be getting intrusive thoughts on her own when's she not occupied, she'll mull over things." Police say that interviewing young Shannon could be a long process, but that "throughout this enquiry our main focus has been and continues to be Shannon's welfare."
Perman-Kerr told ABC News that debriefing people, especially children, following such a long ordeal, requires giving her a lot of space.
"Shannon needs calm words and actions right now, no big parties. Somebody who has been through this is very easily overwhelmed," Perman-Kerr said.
"It's like when you have a bad bout of flu, and when you try and get up and do what you normally do, you quickly realise you're exhausted and you don't feel like talking to anyone," she said. "You just want get into bed again. Anybody who has been in a kidnap situation is likely to feel like that."
Much of the British media, and some politicians, have been asking why it took police so long to find Shannon.
Edward McMillan-Scott, Conservative member of the European Parliament for Yorkshire, said the statistics on child abductions should have led police to check all family members more comprehensively.
"In more than three out of four cases like this a family member is involved, so a thorough search would have included the suspect in this case," he said.
He called for a more wide-ranging review of Britain's procedures for dealing with missing children, insisting that if Britain had a system such as the "Amber alert" used in the United States or similar systems used in France and Belgium, Shannon could have been found within hours of her disappearance.
British law enforcement does have a system like the Amber Alert, but police pointed out that because it is for use "in potential child abductions where a vehicle or partial vehicle details are known," it would have been "wholly inappropriate" to have used it in Shannon's case.
"The suggestion it could have somehow speeded up Shannon's recovery is totally inaccurate," a police statement said.
Police sources defended the amount of time it took to find Shannon just one mile from her home, with a relative.
There were 200 officers on the case and they interviewed members of Shannon's immediate family, and then turned to her extended family, which amounted to hundreds of people, police said.
Police said they had knocked on the suspect's door because they were working their way through that long list of relatives, and not because they had received a tip, as has been reported in some of the British media.
According to Britain's Daily Mail newspaper, one possible factor that took so much police time is that "an astonishing 1,387 registered sex offenders live within a 20-mile radius of the nine-year-old's family home in Dewsbury Moor, West Yorkshire. And with so many suspects within half an hour's drive, police had a huge list to work through."
Perman-Kerr told ABC News that like many other kidnap victims, Shannon may have developed an involuntary attachment to her kidnaper.
"She will wonder what will have happened to the person that captured her, because she may have a feeling of responsibility towards him," Perman-Kerr said. "Often people, particularly children, feel guilt and shame about their part in whatever happens. Very often children will feel that way without telling their parents. Stockholm syndrome can develop in adults, but it's more likely in children."
Police did immediately say when Shannon would be returning return home.