imo, the only time I would ever shout at a child would be if they were in immediate danger - and then, it would be due to my own fear rather than anything else.
I can't think of any other situation when shouting at a child is necessary or even acceptable. There is a tone of voice which a person can use that commands far more authority, and means that the adult retains control of a situation.
Most of us seem to agree that not having tidied his clothes properly is an unjust reason for your nanny to be shouting anyway. But regardless of why she was shouting, I think you should still talk to her about the fact that she shouted at all.
It needn't be specific, or even all that critical, if you're worried of creating any tension. You don't need to tell her you haerd her shouting. You could just catch her at an opportune moment and say sth along the lines of 'I just wanted to talk over DS's discipline with you, so that we're all consistent in his care'. Let her know what you do in various situations, and what you find acceptable.
Otherwise, if she's been with you for 3 months, you could suggest a meeting to review how she's getting on, and slip something similar in there...?
I always appreciate openness and honesty with the parents I work for. Chances are, talking to her will help put your mind at rest, and she might appreciate you communicating with her about your son...