130,000 miles on my FJR and I ride all year long here in the Seattle area with it's constant rain. Never a drop of water in my panniers.
I have overstuffed them and notice a slightly larger seam between the 2 halves - not sure if they would leak then and I can't remember if I've ever ridden in the rain with them overstuffed. To be safe, don't overstuff and you'll be fine.