Wanderers management handed down the punishment to ban the RBB for Sunday's home clash with Perth Glory, in light of flares being ripped within the group at the Sydney Derby on the weekend.
"(Playing without the RBB) Is much harder," Ikonomidis said. "The fans are the heartbeat of the team.
"Away and home games you feel their support. They're chanting whether you're winning or losing.
"It's a great loss for the team. They've been excellent since I arrived at the club a few weeks ago. 
"It's a big loss, hopefully they'll be back soon."
Wanderers were hit with a show-cause notice by the FFA earlier this week following the incident, which is a repeat offence.
The club had previously been imposed with a suspended points deduction which looms with a decision pending.
"Everyone will suffer if points are taken away from the team, the fans and also the club," Ikonomidis said.
"We'll do everything we can to keep all our points that we win oin the pitch.
"In saying that, we won't lessen that support, they're the heartbeat of the club. We want to keep that also."