There are several factors involved, the most significant being speed, weight of the aircraft at time of impact, angle of impact in the vertical, amount of pilot control prior to ditching.
Hitting water is not like hitting a feather bed. The impact can be violent. At takeoff, the aircraft is heavier, and this affects both stall speed--and the kinetic energy when hitting the water. The speed with which you hit the water is a big factor.
Just like in High School physics: Kinetic Energy = 1/2 MASS * Velocity (squared)
If the aircraft hits the water under reasonable pilot control, close to stall speed, in calm seas--then the chances of it being relatively intact are obviously great. Its always a puzzle for the accident investigators, but you would be amazed at the forensics of it all.