Let's see if I can remember everything I've done over the years to my rear wheel.
I've had many problems with my rear wheel over the years. My first issue was when the rim split where the circlip retains the wheel brg. This caused the wheel to flex on the axle rubbing the rotor against the caliper giving a scrapping noise. Had to replace the rim. No warranty. The new rim ran for several thousand miles with no issues. On a cross Canada tour, I had the tire replaced in Edmonton by dealer and several hundred miles later, the wheel started clicking. Rode the bike back across Canada like this until I got home. While removing the axle nut, I heard a loud clicking/ratching noise like something flexed into position inside the wheel. When I pulled the rear wheel, I noticed that the center wheel brg was hard to spin until I removed it from the rim, then it felt good??? All 3 brgs felt good??? Everything looked fine. Why the noise??? I replaced the bearings anyway. A couple of months later, the wheel was clicking again so I loosened the axle nut. This got rid of the clicking but I got that flexing noise again for a moment while loosening the axle nut. When I put things back together, instead of torquing the axle to 81 ft/lbs, I loosened it to around 25 ft/lbs and things were good for a time until I replaced the tire. I noticed another problem. The inner wheel brg on the rim was no longer a press fit but very loose in the bore. It appears the outer bearing race was spinning in the brg bore in the rim. I replaced the brgs again installing with Loctite 638 (retaining compound for loose fits) on the loose fitting brg. I figured that in my effort to get rid of the clicking noise by undertorquing the axle nut I inadvertantly caused the brg outer race to spin in the rim bore. Since then, I've torqued the nut to spec (81 ft/lbs). My clicking noise has disappeared for several years now.
Here are some other things I tried while troubleshooting the clicking problem. I wondered if the cush drive rubber was being over crushed, causing that clicking/ratcheting noise. I tried some lubricant. Not sure if this helped because I also tried loosing the axle nut at the same time... Did the lube get rid of the noise or loosing the axle??? I know
@Rocket Scientist tried loosening his rear axle and had success with clicking. I don't know if it caused any adverse effects with brg races spining in the rim though. Another item is to make sure you use quality brgs. I think
@1olbull posted his failures and successes trying cheap and quality brgs.
Going forward, I still have a rim with a loose fitting brg and I think the Loctite is failing because I'm beginning to get a whine when cornering. I had this whine before and tracked it down to the brg loose in the rim. After the Loctite install (mentioned above), the whine disappeared. That was several thousand kms ago. Knowing I'm going to have to eventually sleeve the brg bore in the rim, I found a practically new rear rim with ABS mount for my bike complete with hub, cush drive and brgs for $100. I also have some new Nachi bearings for this rim. It'll get swapped out when the tire needs replacing or when the whine gets too annoying.
Sorry for the long post but there is a plethora of data on clicking wheels under the search function.