Well, what I meant is it looks odder where you have a lightmap on the transparent water because you lose a sense of it having any volume. The bright spots on the surface of the water call attention to the fact that there should be lighting on some volume inside the water as well, so it ends up just looking like a flat plane suspended in the air. In a modern engine, people would be putting volumetric effects and fog in the water to hide exactly this.
http://scampie.net/etc/transwater_3.jpg
Uniform brightness of the water surface, despite being too bright here, seems to sell volume better. Without the added transparency of the shadowed areas revealing that the light isn't hitting any particles in the water, your mind fills in that the water must be dense. I think if this were simply vertex lit to end up being closer to average brightness of the area it would look fine.
