I don't remember the specifics off the top of my head, but I'm sure there are/have been ~300 yen/h ones in for example Shibuya.
There's a smaller one called Open Source Cafe that lies a 5~10 min walk from Shimokitazawa station - that it's off makes it quiet and nice, and they host meetups from time to time.
The market rate for a fixed-desk designated membership seems to lie around 40,000 JPY / month in the hotter areas like Shibuya and Shinjuku, which is ~20$ per day if you only go there for weekdays. I think that's quite reasonable. I think WeWork has been part of driving this change, but it's definitely overpriced as things are now.