Should you have a water separator? Yes. But the stock 6.9 filter will separate water out of fuel to some extent. The problem is it won’t hold much water, there’s no way to drain it, and there’s no sensor to alert you.
I have dealt with the results of water in diesel fuel. If you get bad diesel from a station, it can come on fast and it’s a killer. We had a guy years ago who got bad fuel at a Pilot truck stop. He made it only about a mile down the road before the truck died. When the water in fuel warning came on he barely made it to the shoulder before it shut down. We had the truck towed to the dealer, and they pumped the tank out. It was about 30% muddy water. It was a Chevy duramax. The bill was right at $9k. Pilot was good about it, they had a leak in their tank or lines, and ground water had made its way in. There were quite a few broken down trucks that day apparently. The reimbursed out towing, and paid the dealer directly. There’s no amount of filtration that’s going to save you in a situation like that. The situations that you can do something about is small amounts of water from condensation or from rain water. Most of my diesel equipment at work gets an extra fuel filter because often times they either sit outside unprotected, or get filled from cans that ride in the beds of trucks etc. it’s a more common problem, so I do more to address it. It’s also important to check for water through the drain on a regular basis. Even if you have the filter capacity to trap all the water, it can cause the inside of the filters to rust.
If you’re interested in changing or adding a fuel filter housing, a decent option is from an early duramax. I just checked rock auto and for a 2009 duramax you can get a GM filter head with a filter, and the water sensor for $112. The reason I bring up the duramax is that it has a primer pump and bleeder screw built in to it. And there’s also the fact that should you find yourself needing a fuel filter at a time and place not of your choosing there’s pretty good odds that one will be available.