You can assign a keyboard shortcut in preferences to open the thought folder in Finder/Windows explorer. I use that whenever I need to “do” something with the files.
There a several bugs that are still open around dragging and dropping files within TheBrain interface. If I remember correctly one involves respecting the preference we have set (it may be fixed by now), I think one is for the keyboard modifiers not being respected on drag-and drop (not fixed), and one involves not giving a duplicate message when moving attachments from one thought to another (also not fixed). They have been in existence for a long time, hopefully they will be addressed at some point soon. I’m not sure how v9 is less “open” than v8, unless you are talking about virtual thoughts and folders. As far as I’m aware, the internal folders it creates and no availability of an api is the same. If there are specific things that you are missing, perhaps enter a new thread detailing them so they can be submitted as enhancements?