Yes, any shore excursions in Japan are expensive whether private or via the ship, however Japan is relatively easy to get around so the shuttles are handy.
Fair enough, we like balcony cabins but some itineraries do not warrant the extra expense. Like you said, if you cannot use the balcony, it is a waste.
They are generally only included on Australian sailings, so most likely not as it is Singapore to Sydney. You will need to check in your personalised or with whoever you booked with.