I doubt it.
The budget traveler won't be affected, mid range travelers going from 200y to 400y if you want/need to stay within city limits if pretty marginal and costs less than staying at a similar hotel in surrounding cities around Biwako or outwards to Nagoya, Osaka, and Kobe and taking the train into Kyoto for the day.
People staying in the upper end hotels probably wouldn't bat an eye at fees if they can afford 100k jpy a night hotel rooms

As mentioned above, I think it'll be more about bringing a bit more money into the city than trying to reduce tourists.