It depends. Usually you'd be right, but for some big events, the stations and platforms can be incredibly packed. In those cases the extra delay from gates could really hurt. One example is Comiket, where you have thousands of attendees all coming to the same few stations around the venue. Both times I was there, there was a massive crowd spanning from the platform to the outside. Having to wait the extra few hundred milliseconds on each card tap would have been painful.
Here's an example video to show the gates in action: https://www.youtube.com/watch?v=YffjxN3KsD4