Yes, there are bolts on the WP that go into water. The three across the top are dry (at least on my R1), the bottom two long bolts go into water and the bottom short bolts go into the timing cover where there's oil. I've never seem them leak but I always put a dab of thread sealer on them too. On the bottom two long bolts it's a good idea to put a little anti seize on the unthreaded part. This way if you have a small leak they won't corrode and gall (dissimilar metals) to the aluminum timing cover.
IMO the best fix for the end bolt holes on the exhaust is to use studs. Coat the end that goes into the head with a good thread sealer, double nut the other end and run them in tight against the shank. Less chance of leaking as compared to bolts.