Your batteries should be fine.
Actually, for storage, cold temps are preferred for Lithium-chemistry batteries, as they then exhibit slower rates of calendar aging than when stored in warmer temps. What you don't want to ever do is attempt to use them while cold-soaked. Charging, especially, in those conditions may cause Lithium plating. And, unfortunately, the BMS' in most small Lithium-chemistry batteries - including ebikes - are pretty crude. I would not trust them to do an awful lot to protect the battery. Just make sure your battery doesn't fully discharge.
I keep the spare battery for my Lectric One out in my sounds-very-similar-to-yours shed, along with the one actually on the bike. My two Tesla's stay out in the cold, too (no garage).
Summertime temps in your shed are when you should worry. That and the fact that you're storing your bike at near full state of charge. When not using your bike, 50% SOC (46-47 volts on a 48v system) will degrade notably slower than a battery stored near 100%.