I can't imagine that there are too many people that can swear to have taken every pee or dump in the appropriate facilities since they were potty trained.
I don't see much difference between a pilot or long distance truck driver or even a motorist on a long journey - when ya gotta go ya gotta go. A question of necessity not necessarily standards.
Sure - if there are facilities on your aircraft then use them unless there is a very good reason not to - but surely if done discretely there are more important things to worry about in this world.
AS