It was the reaction to the threat which cost millions of dollars. We should be careful to distinguish between the costs of terrorism and the costs of our reaction to it.
You might think differently if you were responsible for those children. Do you want to take the risk that it might be a real threat? How do you tell the difference between a real threat and one that isn't real? I'm guessing the people at the school district thought the small risk wasn't worth it, and decided to close the schools. Who would want to be labelled as the person who didn't close the schools if someone ended up getting killed? Even if the threat seems implausible, it must be a very difficult decision to make. There have been many bomb threats recently, probably mostly implausible, but for every one of them the airline acts as if it might be a real threat.
Why a difference in response? A few days earlier, less than 100 miles from the LA school district, 14 people were killed by ISIS-inspired terrorists who also had a garage full of pipebombs. What administrator in their right mind wouldn't be extra cautious with specific threats?