The 27-year-old initially made the switch to the Britannia Stadium on a season-long loan from fellow Premier League outfit Aston Villa in August before making the move permanent in January, though his current deal expires at the end of the campaign.
But Hughes has revealed talks are ongoing to extend his stay, and says Ireland is keen to remain with the Potters.
"Stephen is somebody that we are hoping to keep here beyond the end of this season," Hughes said.
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"He hasn't featured as regularly as he would have liked recently, but that is more down to the form of other players in his position.
"He is a player that I have a great fondness for, he is a very good person to have around the place and we see on a daily basis the undoubted qualities he has in his locker.
"I have worked with Stephen before and I know what kind of impact he can have. He has shown it in glimpses this season, so he is somebody that I would like to keep with me at Stoke City for another few years at least."
Hughes was speaking ahead of Stoke's visit to Carrow Road to face Norwich City on Saturday, and the Welshman revealed he has doubts over the availability of Peter Odemwingie (calf) and Marko Arnautovic (hamstring).
Charlie Adam will also be unavailable due to his three-game suspension for stamping on Arsenal's Olivier Giroud, and Hughes has criticised the process that led to that ban.
"I think the process is fundamentally flawed," added the Welsh boss.
"If the game was reviewed by the people who were actually there on the day, immediately after the game, then any decision after that in terms of possible incidents missed in the game you would accept there was maybe something to investigate.
"The people involved knew the context of the game rather than allowing trial by media. By the time the decision (to ban Adam) was made on the Wednesday I think the agenda was set."