Former captain Hughes was persuaded to reverse his retirement when O'Neill took over the reins from Nigel Worthington at the start of 2012 but there has been no decision yet about how long he might continue.
O'Neill revealed last month that he planned to talk to the 33-year-old defender about taking on one more qualifying campaign leading up to Euro 2016, but those discussions will not be advancing imminently after Hughes aggravated the groin problem that has kept him out of action since the end of August.
That meant O'Neill was not able to name him in a 23-man squad for clashes in Azerbaijan on October 11 and Israel four days later.
The player, who has 87 caps, might feasibly have made his final Northern Ireland appearance but O'Neill is eager to keep him around.
"I hope he hasn't played his last game. Someone like Aaron has far too much to offer," said O'Neill.
"We've asked him to play at right-back during this campaign and he's done that with as little fuss as possible.
"I just hope we can work something out with Aaron. I think he has enjoyed working under myself and Billy (McKinlay, assistant manager) and he knows how important he is.
"We've had discussions and I sincerely hope Aaron will carry on."
Bradford's Rory McArdle is the primary beneficiary of Hughes' absence and has been drafted into the squad as cover.
Palermo striker Kyle Lafferty is another notable absentee from the squad.
He was given a straight red card in the 4-2 defeat by Portugal - earning a severe rebuke from his boss in the process - and while he is banned from the Azerbaijan trip, he is available for Israel.
O'Neill admits he is surprised Lafferty was not given a full three-game ban and has opted against adding him to the group for the second match.
He has been placed on standby but, with no prospect of qualification from Group F, O'Neill has decided to allow the likes of Will Grigg, Josh Magennis and Billy McKay to press their case alongside Jamie Ward and Martin Paterson, who have started the last two matches.
"Kyle is suspended for Azerbaijan and not Israel but we only really got clarification on that this week," he said.
"I had anticipated Kyle would be out for both but as it is he's on standby for the second game. There are no issues, I had a very good conversation with Kyle after the Portugal game and hopefully he's put it behind him."
The size of Northern Ireland's player pool means O'Neill has limited room to chop and change between games and as such he declined to swing the axe after last month's demoralising 3-2 defeat in Luxembourg.
Instead, familiar faces will have the chance to put that result right.
They are bolstered by Chris Brunt, back from suspension, and the fit-again Sammy Clingan.
Chris Baird, who featured from the bench against Portugal despite being unattached but was not required against Luxembourg, is also challenging for a starting berth having signed a permanent deal with Reading.
Winger Paddy McCourt had been left out of recent squads due to being a free agent but can be considered unlucky after signing for Barnsley and getting some much-needed game time under his belt over the last two weeks.
Northern Ireland squad to face Azerbaijan and Israel: Carroll (Olympiacos), Mannus (St Johnstone), McGovern (Falkirk), McAuley (West Brom), J Evans (Man Utd), Bruce (Hull), Hodson, D Lafferty (Burnley), Cathcart (Blackpool), McArdle (Bradford), Baird (Reading), Davis (Southampton), Norwood (Huddersfield), McGinn (Aberdeen), Ferguson (Birmingham, on loan from Newcastle), C Evans (Blackburn), Brunt (West Brom), Clingan (Kilmarnock), Grigg (Brentford), McKay (Inverness), Paterson (Huddersfield), Ward (Derby), Magennis (Aberdeen).