[Wasabista]

As MMM and Sangetsu said, no reason not to bring the cash, Japan is one of the safest countries in the world.

As for ATM fees, they vary quite a bit from bank to bank so be sure to ask, and don't be shy about moving banks. Don't have specific information as I don't have an account at home but I'll ask around.

Exchange the cash for yen at home instead of in Japan, you'll save tons of money.