Seal Cleat opening on Clipless Waterproof / Winter Cycling shoes? I own some Shimano MW7 waterproof cycling shoes I use for wet riding and 45Nrth Wolvhammer boots for deep winter riding. Should I be concerned about water entering my shoe via the cleat opening? 

If so, should I attempt to fill any gaps around the cleat holes to prevent water infiltration (especially from hiking through wet snow in the winter)? Or are these types of shoes typically sealed around the cleat opening from the manufacturer?
You should be concerned yes, because wet feet are not happy feet. 

However, this is something your shoe manufacturer should have taken care of.  I have owned Specialized and Lake brands of waterproof shoes.  I have not ever had problems with water entering through the cleat holes of either (I have owned A LOT of Lake boots).  However, that doesn't mean your manufacturers have the same care.  You could call to inquire, or better yet, test.  

It should be easy to stopper a sink and put the footbed below the waterline to see what happens.  Testing one's equipment is a great way to build confidence in it.