I don't know about real life. You can get a lot more life out of your batteries running at about 1.8 knots. I usually run all night long (12 to14 hours Edit - I meant all day long as I surface at night) submerged around Scapa to avoid planes and my bat still reads 35. Your second patrol you may be alright along East coast. But later on you risk hitting mines there submerged.
Real life-

Probably get better educated post from others in a bit. If batteries are dead the sub would have to recharge up top regardless of weather before snorkles and snorkles might not work in storms either. I suspect what they might have tried is surfacing and then go to Periscope depth every 30 minutes for a hydro check. Could also have raised the periscope just a foot and scanned around, though in heavy waves probably not much help. I really don't know though if the sea is over the conning tower. I have trouble admitting that I don't know so usually just BS