It's difficult to diagnose noises without actually driving the car. I don't see any real issues with Pilots making knocking noises from the front end area. If it happens consistently I would recommend a road test with a technician to try to get it diagnosed.
Did you ever figure out what the issue was? I have an '04 Pilto and im hearing a clikcing noise coming from teh front driver/passenger side. At first it wasnt very loud of often and now its gettign loudaer and more frequent. At first i though it could be a broken CV boot etc... but after more research one of my buddies(Honda parts guy) says it could be transfer case needing a flush. Can thuis be it? If so, where teh hell is this notorious transfer case? I seen something in the inner left wheel well that looks like it can be flushed, it has a drain and fill plug with 10mm nuts, but im not touching it untill i know for sure. What type of fluid should i use? 80-90 or simply Honda VTM fluid?