The Potters missed out on the Portuguese youngster when he opted to join French club Rennes on loan from Benfica instead.
Hughes could not hide his disappointment at the decision of the 21-year-old striker but admitted that the club have to accept it and pursue other targets.
"We thought it would be a footballing decision," said Hughes, quoted in The Sun.
"It seems to have been more about the money involved. That happens, I'm afraid, and you have to take it on the chin and move on."
The Portugal international, who was part of his country's Euro 2012 squad, spent last season on loan at Deportivo La Coruna, scoring four goals in La Liga.