The shinkansen has plenty of space for luggage. The overhead space will hold even a fairly large suitcase, and there are luggage racks and dedicated luggage space behind the rearmost seats. Finally you can just put it in front of your seat as the legroom is insane.
Yeah I always reserve a seat, as that is required if you have large luggage. Luggage in the subway is not really a problem in my experience, it's the same as one extra person going with you.
Plenty is not a word I would use. You need a specific reservation to use the luggage areas near the doors, often they are fully booked.
A group of Vietnamese joined my train last week having just got off a flight from Da Nang to Osaka. They didn't have a luggage reservation, they couldn't fit their medium size cases overhead. They had to store it in their legroom for three hours. It looked pretty uncomfortable even for a 5ft3 Viet woman. I have long legs, I ain't doing that.
Fair, I have a large suitcase and it fit overhead. I've also never had trouble reserving the space and I've also put the luggage in front of me with no issue.
