I've always ran boots to keep the salt off the shafts and it works great. Without the boots, the shock shafts will rust up after just one winter and eventually the seal starts to leak.
When I was younger I was following the trend of "don't use boots, they clog up with mud and debris" until rusty shock rods became worse so I started using the boots to prevent that. I'm a mudder and I have not had any problems with mud or debris getting stuck in the boot and my shock rods do not rust out anymore. I just removed four year old Bilstein 5100's off my Cherokee two months ago, which had the boots on since day one, and they were empty and the shock rod was clean like new.
But for these shocks I won't be using the boots....because they are red. I have blue coils and black jeep. Too many colors. I will get some black boots instead.