I have done the rear fender delete and did not notice any difference. It was easy to do, looks better, and has had no negative impact. I have now also replaced the front fender with a Cycra SuperMoto fender. It's smaller and you'll get more spray, but it has not presented any problems for me. The spray I do notice is off and up to the sides where it doesn't bother me. I installed the Cycra SuperMoto because it improved the stability of my KLR at highway speeds at and in excess of around 75mph. Many folks have argued with me about that, but there is no question that I had a wobble around and above 75mph with the stock fender that completely went away with the Cycra SuperMoto installed. So, it may be specific to my motorcycle, but that was my experience after checking everything else on my KLR.
If you really want to address spray, lowering the front fender is the way to go. There are lots of examples on this forum of that with the stock and other fenders.