That’s not possible due to the fact that ACF uses either display: block; or display: none; for the css that controls if the fields are shown or not and there isn’t any way to transition between the two states. http://stackoverflow.com/questions/3331353/transitions-on-the-display-property.
It is possible to add custom CSS and JS to fields, but I don’t see how this would really help since the existence of the hidden-by-conditional-logic class is what hides a field. Basically you’d need to set the opacity of every field that does not have this class to 100% and set the opacity of the fields with this class to 0% and then you might be able to transition that, but to be honest, I haven’t got a clue if that would work.
