Getting ready for a recent tour I noticed a little play in my back wheel with an intermittent clunking noise as well, so adjusted the cones. The feeling afterwards wasn't perfect, but I put that down to wear and tear, and the noise went away. At the same time I tweaked my shifting.
About 100km into the trip the noise came back, and continued when under effort or especially under heavy braking (disc brakes). The hub was a little loose again, but I had no means of adjusting it and it didn't get worse, though I had some ghost shifting. When I got home I noticed the cassette was wobbling with wheel rotation, though not itself loose, investigated further and the axle was definitely bent. I replaced it and all was well, the ghost shifting had gone. That was at least 1200km on a bent axle and loose cones, mostly laden, but without further incident.
I can't recall an incident that could have bent the axle at around the right time, and surely it would have taken some impact. I'd had trouble getting the cones just right - it would go just too tight when I locked it off, or loosen on a test ride after stripping down the hub and replacing a failed freehub earlier this year. That was without ghost shifting or clunking and I got it stably right in the end. That bike (my Genesis Tour de Fer) takes some knocks but hadn't recently. It uses a QR Deore XT rear hub.
I'm curious, like to learn from these things, and to know what to watch out for. I assume the bent axle caused the loose hub, but could it have been the other way round? Or could the axle have been getting gradually worse over several thousand km?