Haven't many of the non-zero-g challenges been at least partly solved on nuclear submarines, that carry large crews and stay submerged for months at time? Of course there are more challenges, but you do have people living in a pressure canister for long periods.

I think the difference is largely due to the fact that bringing a bit of extra weight isn't as problematic in a submarine as it is in a spacecraft. For example, you always have a water source that can give you oxygen and you don't have to worry about discarding the byproducts.