the phenomenon you are referring to is called 満員電車 man in densha, but it does indeed feel like being in a sardine can. I remember holding the handles above my head so no one would confuse all the grinding for intentional sexual contact.
100% capacity just means that the seats are all taken and there's one person standing for each hand loop. It's amazing and not very comfortable, but 200% capacity isn't all that bad, for short trips.
Lastly, Shinjuku station itself is quite an amazing place; over 1.2 million people transfer through that station daily!