As much as it is painful for the people who lost families that day, 3,000 people is just a pinprick in the world’s population and there have been many events where more died, either from natural disasters or man-made evil.
God knew the eternal fate of everyone who passed that day from children to the elderly. He knows everything that will happen before it happens. Nothing surprises Him. He uses even disasters so that some might repent and turn to Him before it is too late.
God proclaims “I will have mercy upon whom I have mercy and compassion upon whom I will have compassion.”
Much to Jonah’s (and other’s) dismay.