Though utterly dominant from the start, Shelbourne fell behind in a first half of two penalties.
Hughes shot over while Cherry Orchard keeper Declan Woods showed his agility to tip over a toe-poke from Andy Boyle before the Ballyfermot side took the lead against the run of play on the half-hour.
Glenn Cronin clumsily slid into Geoff Doyle inside the area and Mark Hughes confidently sent Dean Delany the wrong way from the penalty spot.
Woods made another terrific save, when touching a shot from Paddy Kavanagh onto the bar, shortly prior to Shelbourne drawing level on 40 minutes when Hughes scored from the spot, after Ian McNeill was somewhat harshly adjudged to have tripped Gareth Matthews.
It remained one-sided into the second half, but Shelbourne struggled in front of goal, with skipper David Cassidy guilty of three misses in quick succession midway through.
But things fell into place for Shelbourne inside two second-half minutes.
Cassidy got free to pick out the unmarked Hughes who headed home his second of the game on 78 minutes.
Substitute Byrne then added a third when drilling low to the net from outside the box.
Hughes got his second for Cherry Orchard on 84 minutes when punishing dreadful defending to loop a header over Delany.
SHELBOURNE: Delany; Matthews, Boyle, Shortall, Fitzgerald; Kavanagh, Cronin, Dawson, Clancy (C. Byrne, 77 mins.); Cassidy (Gorman, 87 mins.); Hughes.
CHERRY ORCHARD: Woods; O’Sullivan (Sheppard, 85 mins.), Notaro, Byrne , McNeill; Collins, Doyle (Murray, 85 mins.), Moran, Cleary, O’Hara (Fay, 85 mins.); Hughes.
Referee: Rob Rogers (Dublin)