If you only hear the noise with the brake on, and not while pedaling and coasting, then it's a good bet that it's brake issue, and not related to the spoke disc, or anywhere near the hub.
Like HillRider I suspect that it's the rim joint passing the shoes, but it could be anything on the rim as it passes the shoes. Also, it might be play in the brake's pivots which click as the joint bumps the shoes.
Try this experiment. Find a hill you can coast down with decent speed. Remove the rear wheel and mount it backward (cassette on left) making sure the chain is over the hub as it normally would be. Push off and coast up to a decent speed and apply the brakes. Is the clicking better/worse or just different, if so it's the rim, and the solution is to use a file or sandpaper on a block to improve the rim seam slightly. Don't strive for perfection as you don't want to remove more metal than necessary, and the brakes will finish the job over time.
__________________
FB
Chain-L site
An ounce of diagnosis is worth a pound of cure.
Just because I'm tired of arguing, doesn't mean you're right.
“One accurate measurement is worth a thousand expert opinions” - Adm Grace Murray Hopper - USN
WARNING, I'm from New York. Thin skinned people should maintain safe distance.