The former West Brom and Coventry striker took his tally for the season to nine with goals after 16 and 45 minutes.
And County's third - after 58 minutes - came when Port Vale defender Lee Collins turned a Ben Davies cross in to his own net under fierce pressure from Hughes.
Vale gave as good as they got in the early stages and even after Hughes had headed in a cross from Johnnie Jackson, they fought their way back on level terms.
Marc Richards fired the equaliser from the penalty spot after John Thompson bought down Lewis Haldane and it was a penalty at the other end that that enabled County to regain their lead.
John McCombe was adjudged to have felled former Vale striker Luke Rodgers and Hughes took responsibility to claim his ninth of the season.