Hughes scored with his first Premier League shot to put Watford ahead on 11 minutes while Hornets goalkeeper Heurelho Gomes denied Cheikhou Kouyate and then produced a superb double save to thwart Marko Arnautovic.
Kouyate fired over at the start of the second half but Watford doubled their lead on 64 minutes when Richarlison finished a counter-attack.
The visitors went close to pulling a goal back but Manuel Lanzini's shot was cleared off the line by Christian Kabasele as Watford ended a run of three straight defeats.
The Hornets move up to eighth place while Moyes's side remain in the bottom three with nine points from their first 12 matches.
Watford: 25 Nov v Newcastle (A)
West Ham: 24 Nov v Leicester (H)