Bicycle Tutor

About 2 months ago I replaced my wheels with new shimano R500's. About 2 weeks ago there developed an ominous clicking noise as I ride coming from the rear wheel. I have a suspicion that it is either a problem with the hub/axle or loose spokes? I do about 15 - 20 miles a day on pretty rough roads, so my wheels take a pounding! - any suggestion on tracking this problem?
Tnx

Either of your suggestions could be the culprit. Squeeze spokes together to see if there is a loose one. Try moving the rim from side to side to check if bearing is loose.
Unlikely but check the cassette / freehub for tightness. As the wheels are new and still in warranty then you could take them back to shop for checking.
I have a back wheel that clicks when | blow the tire up very hard but is quiet when the pressure drops. (This is due to a spoke that can't be tightened and needs changing.)
So, possibly, put more pressure in your tire to check spoke tension. As an afterthought I assume you have discounted the chance of the derailleur top jockey wheel catching the cassette cogs.