Great fridge! You can't beat a butter conditioner, and the space master shelving is super useful in a relatively smaller fridge like yours.
I have always assumed the hole in the door shelf is there to accommodate a tall bottle in the door shelf below it. You'll find it on a lot of different models and styles of Sears (and maybe Whirlpool) refrigerators from the early to mid '60s.
If the door seals are really shot, I'm not sure where you'd find new ones, but I have a feeling that this style and size of fridge was produced for many years, so they might turn up if you do some digging. If you can remove the existing gaskets and clean them up, that could at least buy you some time. I did that on my '57 GE fridge several years ago and the gasket still looks and seals fine. I did have to replace the freezer door's gasket, but that's because it's not a frost free model and I got tired of defrosting it so often.