Mr Mooney, who was 60, was found dead at a house at Knockreagh Lower in Broomfield, County Monaghanat about 06:45 local time on Thursday.
Gardaí said they are treating the house as a “crime scene”.
Mr Hamill, 37 and from Cullaville in County Armagh, died nearby after he was hit by a car at Ballynacarry Bridge.
His death is being investigated as a fatal road traffic collision, according to the latest official statement from Gardaí.
However, Irish media outlets are reporting that detectives believe Mr Hamill had been inside the house where Mr Mooney died shortly before the fatal collision at Ballynacarry Bridge on the Irish border.
Mr Mooney is believed to have died violently, but the cause of his death has not been confirmed.
Police on both sides of the border closed the road in the Ballynacarry Bridge area after the collision on Thursday
Post-mortem examinations on the bodies of both men are taking place at Our Lady of Lourdes Hospital in Drogheda on Friday.
