The scoops are quite small and designed so the drag for them in the water is not more than the aircraft can handle. The forces can be calculated and measured in tests during the design of the aircraft.
You can see the scope of [CL-415](https://commons.wikimedia.org/wiki/File:Bombardier_415_Probe.jpg) and it is tiny.
You can design them so the power that the engine can provide is enough to keep the speed or have the procedure so the initial speed is high enough so the speed you lose during the filling of the tanks is not enough to bring the speed down to close to the stall speed.
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