Yes, a water separating bulk fuel filter is very beneficial. Diesel fuel is really good at holding water in suspension. Fuel water sepatator filters on the engine will extend the life of the high pressure pumping components of the injection pump. No fuel water separator is 100% efficient at water removal. Thus, filter and strip water at every opportunity to provide clean fuel. I am certain that there will be a number who tell you that this is needless, that they did not do such practices and did not see the benefit of spending that money. To each his onw. I am not promoting filters (at least not the ones my company makes) but filtration and separation are important. As engine fuel injection systems are having injectiion pressures escalate to accomodate the need for cleaner combustion, fuel cleanliness and water content are utmost. Some simple screens can remove water that is "free", water droplets. However there is emulsified water that requires much more sophisticated removal through use of special media filters. One of the best is a fuel water separating filter made by Cimtek. It uses a corn starch additive to the media that absorbs many times its weight in water. It is the same principle as the disposable diapers used to prevent really wet bottoms!
The most difficult water to remove is 'dissolved' water in fuel. It may not apply now to many tractors but the HPCR, high pressure common rail, fuel systems are coming. These systems use injection in the range of the mid 30K PSI. Fuel cleanliness and water-free are absolute requirements. Most HPCR systems operating on Cummins, CAT, MTU and even smaller engines are now filtering down to 2 micron at 99+%.
You do not have that issue, yet. But water in even a low pressure system like the distributor pumps is easily seen by rust on internal surfaces of the no pressure sections of the pumps. Rollers and cam rings as well as the pressure pistons of distributor pumps will display scuffing from water as it is a poor lubricant. Plunger and barrel systems like Bosch inline pumps will show plunger scoring from water. There is no repair of such damage, just replacement of these key components.