I don't think that you actually know this. It certainly doesn't state this in the text.
Moreover, "almost certainly" means that some percentage of them would not be sent to hell.
Okay, so God is the kind of person who decides to drown children because their parents are bad because he is so committed to drowning as the means by which to kill people. That doesn't seem like mercy to me. . .
The assumption I'm making is that drowning children because their parents were bad is not moral. Are you disagreeing with this?
Yes, actually, I am. You call it not moral because you look at it from the human perspective of ending their earthly life, but when life on earth ends, a new life - an eternal life - begins. God's mercy to those who are His is calling them home. His mercy to those who don't yet know or love Him is leaving His servants in the world long enough to tell them about His love.
Arguments of this sort always remind me of the fall of Beziers during the Albigensian Crusade. The church called a crusade to destroy the Cathars in France, who among other things did not recognize the authority of the pope. When the city of Beziers refused to open their gates to the papal army attacked the city and stormed the churches where its people took sanctuary. The papal legate was asked how they were to tell the heretic Cathars from their fellow Catholics and he answered, "Kill them all. God will recognize his own." And they were - thousands of men, women, and children.
I don't think that if God had given that same order at Beziers it would have been moral, do you?
You make the common mistake of believing that morality stems from humanity. Once again, this requires a humanistic philosophy, which if you believe the Bible is completely inaccurate.
God is the only lawgiver and judge. What is moral is defined by God, though we often try to impose our own definitions and values on it.
And, once again, it's not about pain and suffering in this world - that will be forgotten in the next. It's about eternity. How do we know that, in the time that it took them to drown, some of these people didn't recognize that this judgment was from God and repent in their last moments, therefore escaping the final destination of hell? They certainly wouldn't have that chance with a sudden, instant death. The idea that for God to cause someone to suffer is evil or immoral is not only anti-biblical, but absurd. If we, as humans, have the right to cause other humans to suffer for breaking the law we imposed upon them without being called immoral, how much more does God have the right to cause the beings that He created to suffer for breaking His perfect law?
God caused Jesus - His own Son - to suffer more than any of those people drowning in the flood ever suffered - and all so that we could obtain forgiveness. Yet so many of us continue to reject Him, and not only that but to blaspheme Him by calling Him unloving and unmerciful. And still He reaches out to us in mercy, desiring that all of us come to salvation.
Additionally, the idea that an act of judgment is devoid of mercy because it involves suffering is also absurd. You would hardly call it unmerciful for, say, a judge to offer a criminal the mercy of a short sentence but still require him to undergo the suffering of a few years behind bars. But for God to allow children to forego an eternity of suffering and cause them to suffer for a few moments instead, you deem that unmerciful (and unmoral). Interesting.