The short answer is that the tax is included in your rate.
The long answer is that depending on who you use to book your reservation, the price quoted may or may not include the taxes and fees. In the case where the price listed does not include the taxes and fees, that is charged to you when you confirm. It's like when you buy from Amazon.com where the price upon checking out will list the cost of the item and then the calculated tax and shipping fee, then the total . You then can many a final decision to buy or not buy.
Usually (but not in all cases) the price includes the tax. Japan does things differently from other countries such as China where a simple chefs salad may be listed as 40 Yuan but after all the taxes it ends up costing over 70 Yuan.
As for room fees, rooms under 10,000 yen per night is not charged a fee. Rooms between 10,000 to 14,999 yen per night is charged 100 yen per night per person. Rooms greater than 15,000, it's 200 yen per night per person. This is on top of the standard consumption tax of 8% and hotel's service charge usually between 10-15%
If you are unsure of the actual total cost, all you have to do is ask the hotel. It's no big deal.