I'm another longtime Lr user who's started having a similar problem (since upgrading to Lr 6.0/ Mac Mavericks 10.9.5). I could use the OP's wording almost verbatim for my issue...except for the part about "showing my subfolders as being in the root directory." Unlike the OP, if the subfolders I request during import are in fact showing up somewhere, I haven't discovered where that is.
In my case the requested subfolder is not created at all, so all the imported files are in the parent folder directory and then must be moved into a new subfolder after the files import (i.e., moved manually to a folder that I must create and eventually locate for Lightroom). Once in a while the import process has worked OK, but lately, I have this failure to create subfolder problem every the time.
I, too, am importing/copying from an SD card (read by my Mac Mini's built-in reader).
By default, the Folders panel does not show the folders in a tree like the OS does. To fix that, select a folder that should be a the leaf of the tree, right-click on it, and select "show parent". Repeat as needed.
Thanks for your comment but I've always been able to see my full file structure in the folders view. Also, I just result my catalog and now LR is working correctly, i.e., new imports are going into their newly created subfolder and the detailed file structure is displayed in the folder view.