The former Everton defender was impressed with Hubertz's input over a season that saw him end up as the club's leading scorer with 13 goals.
Hughes admits he is a little surprised the former Millwall man has been released, but says the decision by Gray is a fact of life at a club with a limited budget.
"Poul scored 13 goals for us, he probably set up the most goals and he is a handful," said Hughes, who sat out the final month of the season with a thigh injury.
"As a defender, you look at him and he is a presence. You don't want to mark people like that, and it is a shame he has had to be let go because he has been superb for us this season and I wish him all the best.
"But we have to look to the future now, and he is not going to be here."
And he added: "Poul is a striker, and they are always paid the best aren't they?
"But we have let a couple of people go now, and there is a budget to work with.
"Gilly (Ryan Gilligan) and Holty (Andy Holt) have been offered deals and hopefully they will stay, and we can also get a couple of good quality players in which will be better for the squad, and better for the team."
Hughes has suffered complications with the injury he picked up at Walsall in March, which was initially diagnosed as a dead leg.
But he has in fact suffered calcification of the thigh bone, and is going to be sidelined from training for at least another fortnight.
"I am coming back in a couple of weeks, and then I will see the doctor and our doc as well, and they will discuss things with Stuart Barker the physio," said Hughes.
"I am going to start training a lot earlier than everybody else because I haven't done anything apart from a little bit of swimming.
"But I am only a young lad, hopefully I can get back quickly and I am already looking forward to next season."
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