Why can be a great question or a horrible question, depending on why you ask why. If you’re asking because you desire understanding, it’s good. If you want justification, it’s bad. If you want justification so you can argue she is wrong, it’s very bad. I’m not saying motive is unimportant, but when you go straight to questioning motive you miss the chance to connect and learn. Going straight to questioning motive is also a good way to cause offence.
On the other hand, when why is asked to understand, it’s a very powerful question. Understanding why your wife dislikes something or wants something done a certain way can help you make life easier for her (and you). Why can also help you understand things from her past that still affect her. Then you can avoid hitting her where it hurts, possibly giving you an opening to help her heal.
In addition to why you ask why, when you ask why makes a difference. If emotions are high or time is short, hold the why for later.