Unless the water or mud is really deep there should be no need to change the fluids afterword. If you spend an extended period of time stuck in the water it might not be a bad idea to as water can sometime seep around worn seals or in to cracked vent lines. If I do get it to mud/water I do grease everything after the trip to relube/flush out any water or grit that might find its way into the u joints, slip yoke, ball joints, tie rod ends, bushings and such. I spend a lot of time washing every nook and cranny in and outside of the Jeep. It is a good idea to change the fluids more frequently in a Jeep that gets wheeled a lot since wheeling is hard on parts and fluids.
As far as alignment goes, unless I detect a problem like pulling, wondering, stiff or loose steering, or unexplained vibrations I don't check it.