Yes, you can still get water in diesel fuel. It happened to me for the first time in 7 years this past winter. Just after newyears the Water in Fuel light came on in the Ex. It took a couple of drainings of the HCFM, a new filter kit, some White Bottle Power Service, and finally a small slug of Red 911 Power Service to make it clear up completely. I also made sure to run the tank almost empty several times before I added any fuel. It took a couple of weeks for the light to stay off....
It also happened to Travis in the original Enterprise. This even came from a reputable, very busy truck stop. He was driving the truck and lost all power. It was below freezing out, and he stopped, took off the fuel filter, expecting to find the start of gelling, and what he found was a fuel filter full of ICE!!!!!! There was so much water in the fuel it actually froze in the filter under the hood. That took him a bit to sort out.... as he had just recently gotten fuel. I think he eventually had to drain all the tanks and start over.
So yes, you need the water separator. It may not happen, but if it does, you will be very happy you have the water block. Water into the IP and injectors is a costly OOPS..... A frozen or blocked filter due to water is a welcome inconvenience if is saves you buying a new IP and injectors, on in my case 6.0 injectors at $200 each..... I was happy to replace the $50 filter that had caught the water........