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.
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 on Saturday, Hughes said: "We will wait and see - we will see how he rocks up tomorrow."
Jones' goals against Walsall were the first he had scored since January and he only managed five in total in 2012-13.
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."
Jones netted his first goal in the 22nd minute when he capitalised on a defensive error by the visitors and fired in, added another nine minutes later by rifling home from close range when the ball dropped at his feet from a corner, and wrapped things up six minutes from time, slotting in coolly after being sent clear.
Hughes felt his team had been slack in allowing Walsall their goal, with Hemmings being allowed the space to finish on 57 minutes, but was satisfied with Stoke's efforts overall.
"At 2-0 up at half-time I think we were quite comfortable," he said.
"Credit to them, they came and certainly tried to make a game of it and got their reward at 2-1.
"There was a little bit of a mistake from us in a key area of the field and we conceded as a consequence, but we were then able to get a little bit more control.
"I made a change, bringing Steven Nzonzi on, and I think that settled us down again and then we were able to take the game away from them again.
"Kenwyne has had a great night with three goals. We are really pleased for him. It is reward for his work in pre-season. He has worked exceptionally hard."
Walsall boss Dean Smith agreed with the suggestion that there had been positives for his side to take from the game, saying: "Definitely - I thought the second-half performance was outstanding.
"We played some really good football and were the main aggressors at times.
"We told them at half-time that we wanted them to be a bit more positive and go and play in their half, which I felt we did."
Stoke are away against another League One side, Tranmere, in the third round.