The squeaking is usually an easy remedy with some brake pad lube. Perhaps they went a little light on it from the factory. Is the "heavy clicking" like a metal on metal click? I have experienced this on certain makes and models of cars, but not motorcycles. The click was due to the free movement of the pads in the calipers. 2nd gen 4-runners did this a lot, and it was normal. Did the squeaking and clicking start at the same time?
Maybe the pads that are slightly out of tolerance, or the lack of adequate lube is also not cushioning the movement? If you are concerned, I would take it to the dealer for inspection. Safely functioning brakes are pretty important.
Could the bedding of the brakes initially have anything to do with it? Typically if you aren't familiar with working on them though, I would consult the dealer first off just to be 100% safe with it. That's the last thing you want failing.
I'd go with what Cheeze suggested. With that mileage and guessing you purchased it from a dealer new, I'd say don't even waste your time worrying about it and let the service guys identify the problem.
Please do forgive me as I forgot to update. The bike went in for its 600mile service and I pointed out the problem to service. Turns out the disk had a *raised* line in it due to a milling error and it had destroyed the pad as well. The dealership contacted Yamaha and Yamaha told the dealership that a bad batch of disks had got out and they were aware of the issue and would cover everything under warranty.