I recently figured out a similar problem. It turned out to be a couple of my rim eyelets. It only made the noise when weight was on the wheel (i.e. I was sitting on the bike, or equivalent), but then I found I could induce the noise by firmly moving the affected spoke in/out. It was not the nipple or spoke threading, which I lubed, but the actual eyelet where it is formed into the rim.
This vintage Mavic (Open4CD) is on my commuter, which gets dirty and wet. I found the eyelets are actually rusting a bit inside, under the rim strip. Probably the next rain would've stopped the noise, but I put a tiny bit of silicone lube on the eyelet. I hope it doesn't seep onto the braking surface.