I agree also - the 2nd picture seems like the way to go. I think I've done this - accidentally. You have to be careful, though, that the subject doesn't swim outside the light cone.... that's a tricky one to gauge because there's a narrower slice of light that's optimal.
However, with the light pointing down on the subject, even with water in front of it being illuminated, it seems like depending on the steepness of the angle, the light on the particles would not ALL be reflected back to the camera. Think of the particles like little moons. Instead of getting full moons reflected back, you might have a sliver like with a new(ish) moon. Like with the WIDE brackets in the picture, the greater the angle, the newer the moon. (it's getting late.... I'm out of analogies, what can I say....)
So, compared to a built-in flash (right next to the lens - full moon), both setups would produce less backscatter. The first might be trickier to pull off with a moving subject.... but I do think it would be more effective - if you can pull it off consistently. Maybe that's why I've only done it "accidentally".