You should never have trapped water in your bottom bracket shell. Drill a small drain hole if one doesn't already exist. The bottom bracket shell has open holes to the seat tube, down tube, and the chain stays. You wouldn't get much water in there from rain and you wouldn't normally submerge part of your frame in water, but there needs to be a way for it to escape just in case.

I wouldn't compare bottom bracket longevity with mountain bikes that see lots of mud and deep water. That's a whole different game.

I prefer outboard crank bearings because the crank spindle has less flex under load.