My best friend is a puppy trainer for Guide Dogs, it is her job to get them familiar with crowds, public transport and the like. I actually asked her this question, and yes they are trained to poop on command, if they cannot master this they will not go on to full guide dog training. If my friend is very lucky she gets to keep the pup (although she has never had this happen, yet), if they fail. She has been a trainer for over twenty years, and we both live in the town where Guide Dogs For The Blind was first started.