Taking water through the snorkel means it's f'n rough out and, if the system is similar to others, the head valve, which closes to prevent flooding when the snorkel goes under, is having problems. The drain for the snorkel is substantial but can't handle a major flood, which on a boat I was on wiped out some fans and electrical equipment when it overflowed the drain.
I doubt if any flooding from the snorkel made it into the battery. Batteries are well protected and if flooded would be producing chlorine gas, which the skipper would have reported. The report said battery system, which means switches, wireing, and controllers which have been known to overload and burn. The battery compartments are marginally larger than the battery, it is used to keep the batteries in place and has barely enough room between the battery and overhead for a man to crawl to check gravities on the cells.
If the skipper was concerned that the boat was in any imminent danger, he would head for shallower water, but what was reported would be a day at the office on a diesel boat in bad weather. Things go wrong on submarines, you evaluate the problem, solve it, and move on. Sometimes you can't see the big picture untill it's too late. Fortunately, most of the time submariners bring back the boat dispite adversity.
Reducing the speed conserves the battery, and considering the weather, they probably did not want to be on the surface untill it calmed to do a charge. Also it gives time to make repairs and possibly get the other batteries on line.
Bob