The flight simulator FS2 is certainly based on the program code of IPACS' RC simulator aeroflyRC, which still supports 3D water.
I have to correct my own statement. aeroflyRC supports 2D water, not 3D water. The surface of 2D water is flat and the waves are simulated by animated textures. 3D water has real 3D waves.
The 2D water of aeroflyRC is transparent. You can see the ground in the shallow water. The animated textures are nice.
X-Plane 11 has 2D water. The water is not transparent, but the water surface is also animated.
MSFS has 3D water and simulates 3D waves.
For me, 3D water is not necessary. 2D water is good, especially if the performance is better. I get annoyed when the whole lake has the same texture. It's not real and looks unnatural. The rippled surface depends on the wind and is different in different areas of the lake.