You can feel the water slowing you down. They are almost certainly designed with the added advantage of slowing the train down.
The water needs to change direction and it gains a large amount of kinetic energy, conservation of energy says that this has to come from somewhere, in the kinetic form from the train. I wouldn't work otherwise. Now, seeing as the mass of the train doesn't change, it must slow down.
I know it's not as simple as that, before someone steps in, but it's a basic argument as to why it must slow the train down.
B&M will have designed the layout, then taken into account the amount of speed lost from the splashdown. At least, that's my best guess.