Data doesn't actually live on a manifold. It's an approximation used for thinking about data. Near total majority, if not 100%, of the useful things done in deep learning have come from not thinking about topology in any way. Deep learning is not applied anything, it's an empirical field advanced mostly by trial and error and, sure, a few intuitions coming from theory (that was not topology).
"All models are wrong, but some are useful" -George Box