Hi.
You'll have to excuse me reviving an almost decade old thread, but I recently ran into a similar problem, and this seems to be the only discussion about it on the entire internet.
I thought I should share the solution for anyone who ever runs into this problem again. Here's to the posterity, forever plagued by the same headaches, yet none the wiser...
If you ride on either WH-6500 or WH-7700 wheelsets and start hearing a pretty loud clicking sound while braking, it most likely isn't the rim joint, but the tire guide screws touching the spokes.
Under "normal conditions" i.e with new-ish brake pads set correctly, the clearance between the tire guide screw and the spokes (which on both of these wheelsets bulge out a bit, compared to normal bike wheels) is 1-2mm at most when braking.
As the pads wear down the tire guides will start touching the spokes, making a rhythmic click click click sound whenever you brake hard.
The solution is simple. Removing the tire guide screws makes the sound go away. Replacing the brake pads might also work, if you feel like doing that.
In extreme cases the brake shoe fin might start touching the spokes. I wouldn't worry about it at that point, I'm still not replacing my brake pads!!