I don't think there are any
problems with the stock breather hose configuration, unless you try to start your bike with the hose under water. Last year, I rerouted the breather hose to up near the steering head and it was more trouble than it was worth. (It made an oily mess of my radiator cover and would kink up. I would have routed it into the airbox, but I couldn't find a hose route that didn't pinch the tube shut.) So I put it back like it was. Just last week, we did about 50 miles of swamp riding. I'm not exagerating when I say that we were underwater for literally 10 of those miles-some as deep as the top of my airbox and I had zero problems with the breather hose sucking in water. I have rerouted my carb vent hoses for deep water so I had no stalling or bogging
problems like everyone
else in our group did. (FYI: the two upper carb hoses are rerouted into the air box and I've teed off of the float bowl
vent hose into the airbox as well.) But there were no issues with the crankcase breather hose. If you stall in deep water, push the bike out of the water before you try to start it. My advice is to leave it alone and worry about something else.