Holt saw an injury-time spot-kick saved by Saints goalkeeper Artur Boruc at the end of a game bereft of chances and quality.
A victory would have taken the Canaries into the top half of the Barclays Premier League table but Hughton feels his captain will shake off the miss.
"He'll be disappointed because he wants to score goals and it's one less opportunity," Hughton said. "But he has been around too long and taken - and missed - too many penalties to let it affect him."
There was a long period between the initial awarding of the penalty and Holt missing from the spot, as referee Mark Clattenburg consulted with his assistant and also dealt with a number of Southampton protests.
And Hughton reckons the waiting period could have helped heap more pressure on to Holt.
"It can do but I think, once you are there, it's down to the goalkeeper who has got to save it," he said. "If the goalkeeper guesses the right way then he has got a chance. He guessed the right way and it probably wasn't one that was heading right for the corner.
"If it is right in the corner, it is more difficult but he gave him a chance to save it."
Only bottom club QPR have scored fewer league goals than Hughton's side this season, a matter that the former Newcastle manager looked to address with the double signing of Luciano Becchio and Kei Kamara in the January transfer window.
But goals continue to be hard to come by for the Canaries, with Hughton admitting it is an issue everyone is looking to rectify.
"I am not going to say that we have been brilliant in front of goal because the stats haven't showed that," he said.
"But we are working hard on it. In the last two games, I have played two up front to try to get those opportunities and against Everton we scored twice.
"We were up against a good side - they have shown that in their last couple of games, even their last couple of away games, playing well at Old Trafford and at Newcastle.
"In the end, we had to makes sure we didn't lose the game but I thought that we had the better chances."
The lack of goals means Norwich currently sit 14th in the table, despite being level on points with every club up to Fulham in 10th.
And Hughton is hoping the next two fixtures against Sunderland and Wigan, teams below them in the table, can help to secure a third consecutive season of top-flight football.
When asked if he was targeting results in both games, Hughton said: "I hope so. Every game is a big game now. We are going into the last nine games of the season and they are all big games."
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