Hughes scored his 20th goal of the season for the League Two side who came within seven minutes of causing a famous FA Cup shock.
But then Scotland sparked Wigan's comeback by scoring for the first time since his £2million summer move from Swansea where he scored freely, meaning the teams must meet again to determine the winner of their tie.
Despite leading 2-0 at the break against Premier League Wigan, County had to settle for a 2-2 draw and a fourth-round replay at the DW Stadium on February 2.
That game will afford Hughes another opportunity to show that maybe he is worth another chance with a bigger club, despite County's lofty ambitions.
"I enjoyed playing against them. I showed people I can still do it at the top - at least I hope so anyway," said former West Brom and Coventry forward Hughes.
"My aim at the start of the season was to score 20 goals, so I'm not sure what I'm going to set myself now."
Asked if he could see himself returning to a higher level, maybe at the end of the season if County fail to gain promotion, he replied: "I'm not sure.
"Every player wants to play at the highest level they can, but I'm happy here for the time being.
"We'll see what goes on here, but if I keep performing the way I do, then who knows."
Ben Davies added a second goal for County five minutes before the break with a dipping 25-yard free-kick, and at that stage the hosts seemed set for a place in the last 16 for the first time in 18 years.
However Scotland then had his say for Roberto Martinez's Wigan side, on his 21st appearance for the Latics.
"It's been difficult these past few months," said the Trinidad & Tobago international.
"I've been playing mind games with myself, thinking 'When am I going to score?'.
"Thanks to the gaffer as he's given me the confidence to keep doing well, to keep enjoying it and play with a smile on my face.
"I've now been rewarded with a goal, and I'm a relieved man, but I have to hope this is the start of something better for me now.
"With goals you gain in confidence, and hopefully my confidence will grow and grow.
"If I get another one on Wednesday (at Blackburn) the confidence will grow again, then I can relax and play my best football."
According to Wigan boss Martinez, the Premier League will now see "the normal Jason Scotland" - the player who scored 53 goals in 105 games for Swansea under the Spaniard.
"Up until now it's been about when Jason would score, but it's never been an issue for me or any of my staff," said Martinez.
"That's because of the contribution he makes to the team as he works really hard, and he holds up the play well.
"So I'm delighted for Jason given the work rate he has put in."
Ben Watson forced the face-saving replay for Wigan with an equaliser in the 83rd minute, although Hughes feels the Magpies are still in with a shout of a shock.
"For us to perform like we did against them, it will give them something to think about in the replay," said Hughes.
"We can definitely have them in the replay. We've nothing to worry about.
"I know they're a good team, but we've got to go there and get in their faces and show them we can do the same thing at their place."
Before then County face a second winding-up order of the season, due to be heard in the High Court in London on Wednesday.
The Magpies managed to pay off the first debt, £400,000 owed to Her Majesty's Revenue and Customs, but the tax men are now looking for a further payment of £600,000.
Chief executive Peter Trembling is due to announce tomorrow the merger of two interested consortia who are set to pump £2million into County, so averting the latest threat to their future.