There is no reason that you need to put anything into the acknowledgements section until it is accepted and you are preparing the camera-ready version. It is perhaps the only portion of a paper's text that can't really be affected by peer review (unless you do something remarkably unusual). Furthermore, some acknowledgements must always be left our in order to maintain double-blind review: for example, funding should be acknowledged in the final document, but grant information breaks blinding.
Thus, I would recommend that you treat acknowledgements just like you treat author information: blank it for blind review, and add it in for the camera-ready after acceptance.