I do my best to keep the BB out but pedals have often gone under completely. (Roadie, not a CX guy. I have no interest in wading through puddles but when riding fix gear, keeping the pedals out is not possible.) If you pack the bearings with marine grease (and use lots) submersion doesn't hurt much. (That stuff is designed to take being wheeled while freeway hot into salt water to launch your boat. Nothing we do with bicycles comes close.)
Ben