"I was never going to allow Stevie to leave and he has repaid that faith," he told the club's official website.
"I don't let players leave my club if I think it would weaken us and that would have been the case."
Hughes has been delighted with Ireland's performances this season and believes he is reaping the rewards of hard work.
He said: "Stephen has arguably been our best player all season. He has put in some fantastic performances.
"He makes some fantastic recovery runs but myself and the coaching staff cannot take the credit for the condition he is in because he worked so hard during the summer and came back with a real determination to show that he wanted to be part of what we are doing.
"He has worked exceptionally hard from day one and is reaping the benefits now and so are we."