Jones came into the Potters starting line-up for the second-round home tie against the Sky Bet League One Saddlers in one of eight changes made by Hughes from last weekend's 2-1 Barclays Premier League defeat of Crystal Palace.
And having been given that chance, the Trinidad and Tobago international reacted emphatically, scoring twice in the first half and then, after Ashley Hemmings had pulled a goal back just before the hour mark, completing his treble late on.
He has been linked with a move away from the Potters on various occasions since they broke their transfer record in 2010 by signing him for £8million from Sunderland.
And asked if Jones was surplus to requirements at Stoke and looking for another club, Hughes said: "Kenwyne is here and is available (to us) and I'm pleased about that.
"People will look, certainly at this performance, and think they would like his services.
"But at the moment we are quite comfortable he is here and pleased he is working hard and playing well."
Jones had last scored for Stoke in January and he only managed five goals in total in 2012-13 from 30 appearances - although just 12 of those were starts.
He sat on the bench throughout the Palace match and was only thrown on as a substitute by Hughes - appointed as Stoke boss over the summer - in the 81st minute of the previous game, the season-opening 1-0 league defeat at Liverpool.
Asked if, had he been out of the first team and then scored a hat-trick like that, he would be knocking on his manager's door, former striker Hughes said: "Absolutely - without a shadow of a doubt.
"He has made a statement and that is what you want.
"I think he is enjoying the work he is getting, that it is helping him and three goals at any level, in any competition, is good by any standards."
Then asked if it should be expected that Jones would play in Saturday's top-flight match at West Ham, Hughes, who has started Peter Crouch up front in Stoke's two league fixtures this term, said: "We will wait and see."
Meanwhile, Walsall boss Dean Smith agreed with the suggestion that there had been positives for his side to take from their loss, saying: "Definitely - I thought the second-half performance was outstanding.
"We played some really good football and were the main aggressors at times."
Stoke are away against another League One side, Tranmere, in the third round.