Sam - one of the byproducts of the operation of an internal combustion engine is water... I would imagine your exhausts would have tiny drain holes to allow for any excess moisture buildup to escape. It is always a good idea, if possible, to go for a decent length ride to allow the exhausts to heat up sufficiently to evaporate the moisture thereby prolonging the life of your mufflers... especially if you have a 4 piper - heat is dissipated far more readily over the greater surface area of the four pipes as opposed to a 4-1 which has all 4 pots feeding the one muffler... hope this helps!
Cheers, Phil