Shawcross is serving a suspension after he was sent off in last weekend's 1-0 defeat at home to Tottenham, having received two yellow cards.
With centre-back partner Robert Huth having missed a large chunk of the season with a knee injury, Shawcross has stepped up with a series of fine performances in the German's absence.
And Hughes is disappointed that the 26-year-old will have to sit out the Britannia Stadium encounter.
"Having lost Robert Huth early in the season, Ryan has had to show a great level of leadership," he said.
"Maybe in a strange way losing Rob has helped Ryan to grow as a captain. Losing Rob was a big blow to us all and we've really missed him on occasions but Ryan and Marc (Wilson) have played well to fill that hole.
"We will miss Ryan tomorrow too, because he is a real leader and it would have been nice to have seen him play in every minute of every game. Unfortunately that wasn't meant to be."
Saturday will also see Matthew Etherington say his farewell to the home supporters, with the winger set to depart the club at the end of the campaign after five years.
And Hughes is hopeful of giving the 32-year-old the chance of some playing time, adding: "I'm conscious of the fact that Matty Etherington has played a huge part in the recent success at the club.
"Of course, it would be fitting to give him the send-off he deserves in front of the supporters. He hasn't been training a lot recently, but we will try and get him involved in some capacity though. I think he deserves that."
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