Like you, I was concerned about the effects of water being pumped into my car along with the diesel fuel. Back in late '70's and early '80's, at least in my area, it was considerable. A friend of mine had some very expensive repairs because of water in his fuel. I installed a water separator on my car soon after I bought it.
It is still on the car, but I now buy my fuel at a station with a high fuel turnover and find very little water accumulating in the separator.
If you can be selective about where you buy your fuel, apparently there are fewer problems with water now than there used to be. Still, it doesn't hurt to have one on the car, just in case you get a bad batch of fuel, but you need to watch it and drain off any water that accumulates to prevent algae from forming in it.