If the vending machines were to be removed, I don't think I'd notice unless someone pointed it out to me. They are pretty insignificant as Derk mentioned earlier. I definitely would like to see them hold other items besides Fresh Water, Lemonade, and Soda Pop. Gale of Darkness had Moo Moo Milk, I wish they could have continued that with the main games. I do like the idea of putting them in secret bases should they come back. That would be cool.
I'd actually like to just see some old random vending machines in the middle of routes and when you check on them either a wild Pokémon pops out or you find a loose item in them.