I was of the impression that they were afraid of the "bomb" going off and only attacked when they had pretty much determine it was fake.
They attacked, imo, without knowing if the bomb was fake.
They found out from cell phone info, [apparently quite early on] that planes were being deliberately crashed. At that point they had no option left but to 'roll' regardless of the bomb, hostages, or lack of weapons.
In one of the last moments before the end, the passenger who remains the most composed through the ordeal (he makes the first phone call) raises the "bomb parts" over his head and crows that it is indeed fake. So yes, they had an inkling that the bomb wasn't real, but moved anyway.