Thanks for the replies, everyone. Even beyond the issue of the men washing overboard (which isn't possible in the game, thankfully), there is the issue of actually making any forward progress. The swells were so large that my props would come out of the water between waves. Then the next wave would come and completely drown the ship. It was actually showing me as being at a depth of 10 meters when the waves would hit. Each time that happened the game thought I was submerging, so the diesels would stop running! I'm sure this would have happened in real life as well as the water came over the air intake for the engines. My depth meter was fluctuating between 3 and 10 meters the entire time I was running surfaced.
I actually ended up just going flank speed on the surface for an hour or two to charge the batteries and try to get out of the storm. My speed, despite running at flank, was just a handful of knots. I stayed on the surface until my batteries were at 75%, then dove to get out of the weather again. I made my way towards the friendly coast and the next thing you know the storm is completely gone and the water is like glass. I didn't keep exact track of it, but the storm lasted all the way from Scapa Flow until very near Dunkirk. I'm guessing about 2 days in game time?
I needed to load my external torpedoes, since I had used all of my internals during patrol. But I was in way too exposed an area to do it right then, even though the weather was now clear with still water. So, I began making my way towards a friendly port (not too far from Dunkirk) where I could stop and bring in the externals. By the time I made it to a safe area, it was storming again.
Luckily, it was just heavy rain and the waves weren't high enough to prevent me from bringing my torpedoes inside.
PS> I've seen Das Boot more times than I can count.