WeWork might be full but there is co-working space all over the city, some of them hourly or daily, most of them are not full at least when I've visited. There must be 50 or more in Shibuya alone.
But anyway, maybe I haven't seen the cheaper Tokyo co-work spaces. If you have some convenient points, I would appreciate a pointer!
Edit: I'm actually in Shibuya every few months. When I'm there I work in the Shizutetsu bus station. If you see a middle aged white guy there programming, come say hi ;-)
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.