This video was made in Holland, which for the most part is under sea level. Meaning they wouldn't necessarily have a choice to put it above the water level. They also regulate the water level with a bunch of pumps and locks in those ditches, many farmers would irrigate out of those ditches so the level would be different depending on the time of year. A drain sitting full of water is not real good for sediment, I agree. That is probably why they do a lot of maintenance to their drainage systems, like in this video. Some farmers do this every fall. 

https://www.youtube.com/watch?v=kAXHbHLQPJE