What the scientists understood was how the energy from the blast would be released in a technical sense — how much as blast, how much as heat, how much as ionizing radiation. They had plenty of experience in knowing how blast waves worked (from conventional explosives), but they had very limited experience with large amounts of thermal radiation (of the magnitude a bomb puts out) and knew enough about ionizing radiation to say what kinds of exposures would be dangerous and deadly.

What they did not know, though, was what would happen when you set such a thing off over a city. Cities are complicated creations, made of many different kinds of materials over vast areas that can be bounded by various natural features like mountains, rivers, and so on. The major Allied experience with city bombings in World War II were what we might think of as very large but very distributed attacks — hundreds of planes carrying bombs that contains incendiary bomblets. So lots of little fires and explosions over a large area, as opposed to one very big explosion. And yes, they knew "it would do a lot of damage," but they wanted to know how much damage. Would it create a firestorm? How much blast pressure do you really need to destroy a Japanese house? What exactly would the radius of destruction be? How deadly would it be compared to firebombings? An atomic bomb attack, despite having many ethical and superficial similarities to a firebombing attack, is not the same thing — the effects are different and are distributed differently.

They attempted to get a rough sense of it by looking at the closest analog they could think of, which were cities destroyed by accidental ammunition dump explosions. So they were very interested in the Port Chicago accident of July 1944, and they were also interested in historical accidents like the Halifax accident (1917), as both of these gave some data on what kind of devastation to expect (even though their releases were still far less than nuclear — Port Chicago was around 2 kilotons, Halifax was around 3 kilotons, whereas Hiroshima was 15 kilotons and Nagasaki was 20 kilotons).

They figured that the blast would be the major effect of the bomb, and so made their plannings around that. They made no serious effort to calculate casualties. They assumed that anyone close-enough to the blast to be killed by ionizing radiation exposure would be close-enough to be killed by blast or fire. They seem to have been genuinely shocked at the exact magnitude of the deaths at Hiroshima and Nagasaki, and further surprised that radiation played a significant role in the deaths. For more on casualty estimates and their surprise, see my article here. It is of note that the atomic bombs turned out to be significantly more (like 4-5X more) deadly per area affected than the firebombing attacks, so any metric of estimation of casualties based on previous attacks was going to be off by a lot.

So while on the one hand they were very much trying to destroy entire cities to create a psychological spectacle (these were their explicit, stated aims), on the other hand in retrospect they really were unsure about how it was going to play out in practice. One consequence of this is that the US Army sent survey teams to Hiroshima and Nagasaki immediately after Japanese surrender in order to do comprehensive survey of the damage (physical, biological, even psychological) of the bombings, because these were the only "experiments of opportunity" that they had for understanding how this would work out in the "real world."