Pete,
On stream crossings, I remove the bags, portage the bike across on my shoulders, then go back and do the same for the bags, then reassemble on the far side. As many trips as it takes. For me -- personal choice -- it is just not worth it to submerge the bearings and frame tubes and pay the consequences for it midstream (so to speak) on a remote tour.
It might well be fine or one might get away with it, but what if you don't? Is it really worth it to ride with water-contaminated bearings or start rust in a SON dynamo?
All the best,
Dan. (...who errs on the side of caution and so won't swim a bike)