I think you'll find that they are simply throwing back your lazy method of enquiry.
It's quite possible the people you are working with are feeling personally attacked when you walk around questioning what they are doing. People don't like to have themselves questioned for no given reason. Saying "Why not?" is a low-effort way to move the onus for explaining themselves back to you.
Simply asking "Why?" demands that the person being asked must now completely justify their method/opinion/etc. It makes it sound like you are disapproving of their current method/opinion (whether you are or not), but have not completely thought through your own opinion of it.
It also comes off as aggressive, as you have essentially thrown doubt upon an otherwise (in their eyes) perfectly acceptable method/opinion, and demanded a justification from them, which they may not be prepared to give, either because the explanation is long and complicated, or because they did not decide upon the method in the first place, having learnt it from someone else.
I know that I've personally been asked "Why?" by a boss who has already decided that they don't care why, and are planning to tell me to change my current methods. In that case, I was annoyed that I was demanded to explain myself, and immediately have that explanation ignored anyway.
Instead of looking for whitty retorts, you might find it more valuable to invest your time in asking constructive, non-aggressive questions. Something like "Why do you use [method 1] over [method 2]? Is it [faster/easier/more precise/etc.]?". You will find you get much more direct answers, and eliminates "Why not?" as a possible response from the start.