Premier League clubs are only allowed two loan signings from teams in the same division and Stoke have already brought in winger Oussama Assaidi from Liverpool.
Ireland has scored three times in 15 appearances for Stoke this season and Hughes wants to agree terms with Villa as soon as possible to create a vacancy for another domestic loan signing.
"We're looking into that (permanent deal) for Stephen, that's the intention," said Hughes.
"We've had conversations with Villa and we would like it to be concluded. If it does happen it frees up another loan for us domestically that would give us a bit of flexibility, which would help.
"We'll try and use that loan in a good way. We'll be pleased if it does come off and there's no reason to think it wouldn't.
"If Stephen does join permanently that's credit to him since he's been here because he has done very well."
Assaidi has also been hugely impressive for Hughes' side, scoring three times in Stoke's last six Premier League matches.
Hughes said no discussions have taken place with Sunday's opponents Liverpool regarding the Moroccan's future, but admitted his side are in the market to strengthen in January.
"It's fair to say we're in the market for some players, but I wouldn't confirm or deny any names," said Hughes. "Like everybody else we're trying to get an understanding of what's out there and we've done some work on a number of players we think we can progress with.
"But if you flag somebody up, that can highlight those players to other people and it's a dog-eat-dog situation in January.
"Sometimes you can find you lose a player by virtue of people knowing about them. If you throw petrol on the flames you can sometimes get burned.
"So we'll be playing our cards close to our chest."
Watch Stoke take on Liverpool live on Sky Sports 1HD at 4.10pm on Sunday.