The in-form French striker netted in the 24th minute and doubled the lead with a superb solo effort just after the restart, making it eight goals in his last six matches.
"We are used to looking at Cristiano Ronaldo's statistics but Benzema has now scored 19 goals (in all competitions), which is an important quantity," Real director general Jorge Valdano told Spanish television.
"These numbers are proof of how good he is. He is going to give us a lot to be happy about in the future."
Third-placed Valencia's midweek exit from the Champions League appeared to have taken its toll as Unai Emery's side slumped to a 4-0 defeat at struggling Real Zaragoza.
The Hercules game had never promised to set the pulse racing, with both sides more concerned with battles to come - Real's in Europe and Hercules's to avoid relegation.
Real's quest to reach the Champions League quarter-finals for the first time in seven years requires them to build on a 1-1 first-leg draw against Lyon at the Bernabeu on Wednesday, and Mourinho's line-up reflected that.
Hercules, La Liga's worst travellers with only six points and three goals scored on the road, were without injured top scorer David Trezeguet while his strike partner Nelson Valdez only came on midway through the second half.
It did not take Real long to breach the visitors' defence, Mesut Ozil sending Alvaro Arbeloa down the right, from where he pulled the ball back for Benzema to sweep home the opener.
