The Swiss international has only just returned from an injury spell and Stoke will be keen to wrap him in cotton wool ahead of the Hammers clash.
He was replaced by Egyptian teenager Ramadan Sobhi and it was the substitute's cross that Swans defender Alfie Mawson turned into his own net to restore Stoke's lead.
Hughes lauded his summer signing but warned he will continue to slowly expose him to the Premier League.
"I could have put more senior players on because it was quite early but I just felt Ramadan was ready," he said. "It was a good home game for us and the opposition was the right opposition. I was really pleased with his output.
"He's only 19 and made a big leap of faith coming here, but he's got a lot of experience. He's played 60, 70 games in senior football in Egypt so he knows his way around a pitch. His physicality is good enough as well so that helped him.
"We've got an exceptional player there. He won't play every game, we will use him sparingly. You sense when you've got an option like that, at some point you have to use him."