How can I stop my feet/shins getting soaked/muddy when cycling offroad in the winter?
I've never had a pair of MTB shoes that are waterproof though I wouldn't doubt if they exist. Even if they were you'd still have water coming of your shin and into the shoe (this is what makes even waterproof shoe covers a bit wet inside).

I just tough it out. I have a set of neoprene shoe covers that keep my feet warm and maybe even dry depending on how wet it is. I have a set of full length tights and a set of leg warmers. If either of those are dirty I just hose them off when I clean my bike at the end of the ride and let them dry. I'll wash them every few rides.