The plant that I often work in has an underground 4.16kV distribution system. The number of cable failures was drastically reduced after we installed sump pumps in all of the manholes. Yes, the conductors were suitable for wet locations, but it seems they last longer if they are not always underwater.
I would think that it would be safe to pump the manholes out while the conductors are energized as long as you do not enter the manhole to do the pumping. I would expect that you could remain outside the arc flash radius and drop the suction hose in to the manhole. I would want to do some type of check to make sure the water was not energized before I did that, but I think if there was enough leakage current to energize the water, you would have already had a cable failure.