Hello there, I'm a newcomer to this forum!
I'm Japanese and have been a H lover these 5 years(newbie, I know). I live in Tokyo.
My honest impression is, for at least this past year, bags (not even non-QB) have become very scarce in H stores.
As some people have observed, the 'display only' bags have become the norm, and I haven't seen many bags that you can buy freely at the store. (I think I saw one picotin and Lindy 26 last year, and the new canvas tote bags, but that was about it)
The Ginza, Omotesando, and Marunouchi store are probably your best bet as the sheer number of bags that will probably be allocated, but because there will be a higher percentage of people flocking to the flagship stores, it will probably be pure luck if you can get a bag. The department store shops usually have less stock, but because the customer number are a bit less, you MAY have a chance of finding something. (BTW Shinjuku Isetan is a very different story compared to other department store shops. I feel it's more close to a flagship store)
If I was visiting Tokyo and had free time, I would probably hit the Ginza store first, try Shinjuku Isetan and Omotesando, and if I had extra time would go around the department stores. But I think for the time being, the chance of getting a QB easily in Japan might not be realistic for now.