With the Potters 2-0 up in the Carling Cup third-round tie at the Britannia Stadium, Wilkinson received a booking in the third minute of stoppage time for bringing down Dembele, who clutched at his left leg and had to be carried off on a stretcher.
The Belgium forward departed the stadium on crutches and Hughes was left wondering what Wilkinson could have had been thinking when he made the tackle.
"The next 24 hours will show us how bad the injury is," Hughes said.
"If he has avoided serious injury then he has been a very lucky boy because the tackle that took him out was, from my point of view, an absolutely ridiculous challenge at that stage of the game.
"When you are at that stage of the game and your team is leading 2-0, there is a certain code I would suggest that you look after your fellow professional, and the lad has ignored that.
"There was no need for the challenge at that late stage in the game and he has put a fellow professional's career at risk by the nature of it. I don't know what the hell he was thinking about to be perfectly honest.
"We are hopeful that he (Dembele) is fortunate and there has been no break, and if that is the case, it's a blessing because at the time of the challenge I thought he had done a real serious injury."
Fulham's England striker Bobby Zamora recently broke his leg and Hughes admitted losing Dembele - scorer of three goals since his arrival from AZ Alkmaar last month - for an extended period would leave the Cottagers seriously short up front.
"We have already lost Bobby Zamora to a serious injury and will be five months at least with him out of the side, so we can ill-afford to lose another quality striker," Hughes said.
"We have been really pleased with what Moussa has produced in the short time he has been with us and if we have to be without him for any length of time then that is going to compromise our attacking threat."
Stoke assistant manager Dave Kemp agreed that Wilkinson's tackle had been unnecessary but insisted the defender had not meant to harm Dembele.
"It was an unnecessary, rash challenge - we know that, we are football people as well," Kemp said.
"We have spoken to Andy about it. He didn't need to make the challenge, I agree.
"All I can say is that I hope the player is not too badly hurt.
"There is no malice in his challenge - it is just over-enthusiasm."
Referee Mark Halsey blew the whistle for full-time shortly after the incident to confirm the hosts' victory and their place in the fourth round, which was sealed by headers from Danny Higginbotham and Kenwyne Jones in either half.
The Potters team featured seven changes from their previous outing and Kemp felt the result demonstrated the strength Stoke's squad now has.
"I don't think we weakened the team," he said.
"Like a lot of teams in the Premier League we have a good squad.
"We had good defenders on the pitch tonight, good midfield players and good forwards so that we could score goals.
"This is probably the first time this club has been in a situation like that."