What happens when a bomb threat is received in an office, or shopping mall, or a passenger terminal? We evacuate first, often heading for a nominated assembly point.
Except for the people in the same room as the one making the threat. The people in that room are his bargaining chip. He's not going to let them leave. Witness other hostage negotiations, because that's what this effectively is.
Unless people are getting hurt, the aim is to get everyone out safe, usually including the perpetrator, and however long that takes is how long it takes. If things start going south, that's when other options need to be explored, right up to the point where collateral damage becomes acceptable if it prevents further violence. In this case, it appeared that there was no immediate danger to the passengers and crew, so a low level peaceful resolution could be implemented. Which it appears is what happened. So it took 3 hours.....so what?
Everyone walked away in one piece.