You answered your question, actually.
Rubbing/popping noise may be coming from the top hats, or even from the steering rack. For instance,there was a recall for 2006-2011 Civics, the reason was they didn't torque rack and pinion bolts properly, causing popping noise. Yours is not a Civic though, but obviously Honda's steering racks are not the most reliable one on the market.
Change the endlink first and see if there is still any noise.