Zamora is struggling with an Achilles injury and is a doubt for the biggest match in the Cottagers' 131-year history.
A clearer picture over his availability should emerge today and Hughes feels it is imperative the team's top scorer features after playing such a central role in helping Fulham reach the Hamburg Arena.
"Bobby's desperate to play. It's a European final and he's contributed so much the club," said the Northern Ireland defender.
"This season he's had the goals to go with his hard work whereas last season he didn't get the recognition he is now for scoring.
"Everyone's delighted that he's been able to get the recognition he deserves. He's such an important part of our team.
"If he doesn't play we'll miss him but fingers crossed he'll be fit and if he is that's definitely a plus for us."
Atletico are clear favourites to prevent Fulham lifting their first major trophy but Hughes insists there is one last effort left in their fairytale season.
"We've done it the hard way in getting to the final and that shows our character more than anything," he said.
"We kept believing in ourselves and the way we play and that's got us to where we are. There's no reason why we can't win it.
"Atletico are such a big name with such big players that we have to be the underdogs
"It's a fine line because anything can happen in the final. It's impressive to get this far but it would be great to win it."
Hughes lavished praise on manager Roy Hodgson, who has become hot property after masterminding Fulham's spectacular campaign.
"Roy's about hard work, about getting across his principles on style of play. Everyone knows their job and their position," he said.
"He's seen it all in his career so is very composed - he knows how to deal with situations.
"He's pretty calm and that transfers to the players. You don't see us panicking much in games, we just stick to the plan.
"He stresses that win or lose a lot can be made of one game when in fact you play 38 in the league alone."