A question about clothing removed by water-wouldn't it be more likely to be completely removed if there were strong currents in the water-rivers, oceans, etc? It seems like the water here would be relatively calm compared to that and that there would be something left on her. A sock, underwear, something.
The question about clothing- yes oceans and swift-moving rivers/currents are more likely to remove clothing quickly and violently. But take into consideration the physics of an underground city water system. The pressure of the water is hugely increased due to the varying sizes of the piping used to control water. That will increase or decrease speed and velocity.
I think it is entirely possible that after being whirlpooled repeatedly that clothing could be removed. Not saying that is necessarily the case here. But I do think it is possible.