I bothered me a little, but I considered it to part of the whole undersprung and underdamped package, which I was going to change anyway.
You've been riding your EX for about a year already, and just noticed it? If so, I would just just ignore it.
The fork should not come apart, I think. I've had a WP fork on my KTM 1190R clunk as well. I do not know if this clunking is a WP thing or a soft suspension thing.