Yes, the stock 4CS has not enough damping and it clunks on both the EX and MX. Revalve it to increase the damping and it will be good. You may also want to try using the clickers to see if they would partially help.
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.