There was a touch of good fortune about Stoke's winning goal as from Xherdan Shaqiri's 29th-minute corner, Adam's downward header struck the foot of the far post and bounced along the goal-line, hitting Hornets goalkeeper Heurelho Gomes on the knee and rolling into the net.
Hughes had been hit by injuries to Ryan Shawcross and Glenn Whelan as well as a suspension for Joe Allen, but felt his patched-up side were deserved winners.
"I thought we were good value at the end," he said. "Charlie was excellent. He had to be more disciplined than we usually demand of him. Usually he has a defensive midfielder alongside him but he did not have that option.
"I'd have to see the goal again before I can say if it is right or not, but the key thing from our point of view is that it is a winning goal."
Hughes was however unimpressed with Watford boss Walter Mazzarri left him hanging on the touchline after snubbing his handshake after the final whistle.
"I'm a little disappointed," he added. "It is something maybe the foreign managers don't always do and they need reminding it is something we do over here.
"Mind you, British managers are in a minority these days so maybe we shouldn't expect it.
"It was an emotional game and I think he was a bit emotional afterwards. He needed to be reminded, and I've shaken hands with him since."