1/4 is very thin, thicker is highly recommended, BUT if you personally for sure absolutely feel that your 3/4 inch sub floor is level and smooth and strong enough then go for it. I would not do this in my house though.
Then, we may have a symatic question here, but you said mortar as the medium, I think you mean thinset. Use whatever medium is more convenient for you, dry or pre mixed.
Before you apply this 1/4 cementious board, hear from others that will respond.