Jones came into the Potters' starting line-up for the second-round home tie against Sky Bet League One outfit Walsall in one of eight changes made by Hughes from last weekend's 2-1 top-flight defeat of Crystal Palace.
And having been given that chance, the Trinidad and Tobago striker 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.
Jones sat on the bench throughout the Palace game and was only thrown on as a substitute by Hughes - appointed Stoke boss over the summer - in the 81st minute of the previous game, the season-opening 1-0 league defeat at Liverpool.
He has been linked with a move away from Stoke on various occasions since the Potters broke their transfer record in 2010 by signing him for £8million from Sunderland.
Asked if Jones was surplus to requirements and looking for another club, Hughes, who has started with Peter Crouch up front in Stoke's two league fixtures this term, said: "Kenwyne is here and is available (to us) and I'm pleased about that.
"People will look, certainly at his performance tonight, 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."
And when asked in his post-match press conference 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 tonight and that is what you want.
"I thought it was important that I respected the other guys in the group, so I made a number of changes in different areas. Kenwyne came in up front and played exceptionally well, I thought.
"His link-up play was good tonight - at times it can be a little bit loose, but I thought it was better tonight.
"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 against West Ham on Saturday, Hughes said: "We will wait and see - we will see how he rocks up tomorrow."