The latest rulings come 19 months after the court concluded that Sheikh Mohammed had abducted two of his daughters, mistreated them and held them against their will.
"The findings represent a total abuse of trust, and indeed an abuse of power to a significant extent," Judge Andrew McFarlane, President of the Family Division in England and Wales, said in his ruling.
The sheikh rejected the court's conclusions, saying they were based on an incomplete picture.
"I have always denied the allegations made against me and I continue to do so," he said in a statement.
"In addition, the findings were based on evidence that was not disclosed to me or my advisers. I therefore maintain that they were made in a manner which was unfair."
Sheikh Mohammed, 72, and Princess Haya, 47, have been involved in a long, bitter and expensive custody battle since she fled to Britain with their two children, Jalila, 13, and Zayed, aged nine. She said she feared for her safety amid suspicions that she had had an affair with one of her British bodyguards.
"It feels like the walls are closing in on me, that I cannot protect the children and that we are not safe anywhere," Princess Haya told McFarlane in a statement. "I feel like I cannot breathe anymore; it feels like being suffocated."
Among those targeted by the hacking was Princess Haya's lawyer Fiona Shackleton, a member of Britain's House of Lords who represented British heir-to-the-throne Prince Charles in his divorce from his late first wife Princess Diana.
The activity came to light in August last year after Ms Shackleton was urgently tipped off by Cherie Blair, the wife of former British Prime Minister Tony Blair, that she and Princess Haya had been hacked, the court was told.
Ms Blair is also a prominent lawyer who worked as an external adviser for NSO.
At the same time a cyber expert from the University of Toronto's internet watchdog Citizen Lab, which researches digital surveillance, also alerted Princess Haya's lawyers after tracking the hacking, the court heard.
Once the hacking was uncovered, NSO cancelled its contract with the UAE, Princess Haya's lawyers said. The Israeli firm said it could not immediately comment on the case, but said it took action if it received evidence of misuse of Pegasus.
Ms Shackleton and Ms Blair declined to comment.
Sheikh Mohammed is regarded as the visionary force behind Dubai's ascent into a global commercial hub. He has sought to burnish the Gulf city's reputation on issues such as human rights and equality.
Long, expensive battle
Reporting restrictions on Mr McFarlane's findings after a year of hearings were lifted on Wednesday.
"I do not feel that I can move freely forward as things stand now, while I am and feel hunted all the time, and I am forced to look over my shoulder at every moment of the day," the British-educated princess said in one witness statement.
The legal costs of the case have run into millions of pounds, with the case involving some of Britain's most prominent lawyers. The costs of one appeal alone was cited by the court as costing 2.5 million pounds.
The sheikh, who is vice president and prime minister of the United Arab Emirates, initially sought to have the children brought back to Dubai but has since suffered repeated defeats in the English courts.
In a judgment released on Wednesday, Mr McFarlane ruled that the children should live with their mother.
In a ruling published last March, the judge concluded that Sheikh Mohammed had subjected his ex-wife to a campaign of intimidation that made her fear for her life.
He concluded the sheikh had arranged for his daughter Shamsa, then aged 18, to be kidnapped in 2000 off the streets of Cambridge in central England and flown back to Dubai.
The judge also found it was proved that Sheikh Mohammed had arranged for Shamsa's younger sister Latifa to be snatched from a boat in international waters off India by Indian forces in 2018 and returned to the emirate.
Princess Haya's lawyers told the court that the British Foreign Office had been made aware of the hacking allegations, and police had expressed a desire to interview Princess Haya and her lawyers as victims. Reuters was unable to establish if this took place.
London's police said detectives began a five-month investigation last year after receiving allegations of phone hacking. But in February, the investigation was closed because of a lack of "further investigative opportunities".
There was no immediate comment from the foreign ministry.
In his statement, Sheikh Mohammed said it was not appropriate for him to appear in court himself and neither the UAE nor the emirate itself were party to the case and so could not participate.
Instead of showing any concern for the safety of the mother of his children, "he has marshalled a formidable forensic team to challenge the findings sought by the mother and to fight the case against her on every point," Mr McFarlane said.
He concluded, and the Court of Appeal agreed, that the sheikh had authorised the hacking of six phones which took place between July and August 2020 when a vulnerability in Apple's iPhone systems was exploited.
Expert cyber analysis revealed that on one occasion 265 megabytes of data were downloaded from Princess Haya's phone, the equivalent of 24 hours of voice recording or 500 photos.