Manuel Pellegrini's men have fallen seven points behind Premier League leaders Chelsea at the top of the table following a disappointing 1-1 draw with Hull City last weekend.
Stoke may be confident of completing a double over the defending champions after claiming a 1-0 away win back in August.
Hughes feels the absence of Yaya Toure - who will not feature despite returning from the Africa Cup of Nations - has been key to the visitors' recent disappointing form.
But the Welshman expects City to turn things around in the near future.
"You do miss key players, and we can vouch for that because we have lost a number throughout the season," Hughes said.
"Manchester City are no different. Losing players like Yaya for a while is difficult.
"Manchester City have the capacity to replace players like him with other world-class players. They have gone through a difficult period, and not picked up as many points as they would have liked, but they will be ready for this game.
"Top teams and top players bounce back very quickly and we are mindful of that."
Stoke's hopes of another surprise win over the title contenders have been hit by further injury blows, with Hughes confirming that midfielder Stephen Ireland and defender Marc Wilson are both out.
"We are having a period where we are picking up injuries," he added. "Stephen Ireland picked up an injury and isn't available. Marc Wilson has a tear too, and he is out on Wednesday.
"Hopefully he will be ok for Saturday. Ryan Shawcross is progressing but won't be available tomorrow, and neither will Erik Pieters. Saturday [against Blackburn Rovers in the FA Cup] may still be a little bit too soon for him as well."
'Obviously Messi is the best player in history and being compared to him means that you're doing things right, but I try to be myself': Barcelona star responds to comparisons with Argentine legend
'Darwin Nunez would be gold for Arsenal': Liverpool legend claims Gunners should have signed Uruguayan striker in January
