I've been to Japan 5x and taken used Shinkansen maybe 3 or 4 of those trips, I've never taken Nozomi trains (Japan Rail Pass is ineligible) but I've never had trouble w/room for my large suitcases at the ends of each car. There's usually some room behind the last row of seats.

I agree that I wouldn't want to put a huge suitcase overhead.

About the worst case is that it's in aisle.