The gaiters are not a standard R65 part, so you won't find them on the parts fiche for our model. Try Capital Cycle or Bob's BMW for replacements.
I'm no guru, but I surmise that the gaiters do give more protection to the shock assembly, simply from the fact that they keep the travel length of the stancion covered up, keeping grit, moisture and whatever else off the metal away from the seals. I like the look of them, but they probably a good bit more than the little standard dust caps.