Originally Posted by Simbeline
Anyone know if kobo/sony/kindle can/can't deal with subfolders?
They can. They do read books from inside subfolders and display them in a simple linear list
OK, OK ...
This is not the answer you wanted to hear, so here is better one:
Kindle Touch can deal with subfolders, and actually use those for book navigation. Just install Duokan on it. Duokan is alternative Chinese firmware. I have installed it for a friend. Just check what firmware your new Kindle Touch has and do not connect it to internet. You might have problem installing Duokan on Kindle Touch with the newest firmware.
SONY can deal with subfolders and actually use those for book navigation. Just buy T1 or T2 model AND root them. Then you can install quite a few Android reading applications and file managers. T1 and T2 models are Android devices.
Also older Sony readers, most notably PRS 505 had interesting third-party hacks available that let you use subfolders.
You can also root Nook Simple Touch.
Using Android on it is not a pleasure, but an ugly hack, but, once you open FBReader or CoolReader, you do not need to interface with Android that wasn't built with e-ink screen in mind and. Those two reading applications are nice and can deal with hierarchical directories.
From devices that support hierarchical directories AND many book formats "out-of-box" I would recommend PocketBook.