Food lasts 30 minutes. If you are doing a leve that somehow even takes the full 30 it isn't like those extra 98 food are doing you any good. No real reason not to stack them, IMO.

Same logic really can go for potions too. They are so marginally useful, having 99 isn't really going to break anything. I promise you'll be dead before you can use them all if you happen to find yourself in the rare situation in which a potion/ether is needed.