You can't eliminate the clicks, but you can noticeably quiet them down by adding some more grease to the pawls (this is why some are noisier than others). Use the recommended Nexus white grease, or something similar, which is kind of creamy and buttery. Using a grease that's too thick, and/or sticky can mess up the performance of the hub.
I will add.... if you do re-grease things with the Nexus white, avoid using it on the brake shoes, or you may introduce brake squeal. I've had good results using "Slick Honey" grease, for internals and brakes, in Nexus 3's and 7's. A mechanic at one of my LBS's is religious about using Park Polylube 1000 when overhauling Nexus 3's, although I've never tried using it myself.