All the suggestions regarding regular food have already been given, I just would like to add that it's not hard to find whey protein in Nagoya.
I live in the center and I have the following suggestions:
- Sport Depo: this is a sport shop located about halfway between Nagoya station and Kanayama. I can look up the address if you want
- Pacific sport club (
http://www.pacific-s.co.jp/sites/access.html): it's a gym located between hisayaoodoori and takaoka, open 24 hours.
Both of them sell whey protein, Sport depo is a little cheaper though.
There's also a martial arts/boxing shop in Oosu, I know they sell prot but not sure whether they have whey. I can check out if you're interested.
And I'm pretty sure there are tons of other places where you can get whey prot but I've never searched.
Anyway, let me know if you want more details.