I should have mentioned that I'm using Atari800Win Plus v2.8, which supports eight drives and four hard drives.
I had already tried the cold restart after "putting" a disk in drive 3 (and having disks in drives 1 and 2). D3-D8 simply aren't seen. I don't know why. Perhaps a bug in this version of the emulator?
As for the hard drive, I've also already tried cold restarts, typing H:, H1:, H:*.*, H1:*.*, and typing the names of specific files I know to be there, but it returns nothing (though, as I mentioned, the files will still load).
Interestingly enough, if I point the hard drive to a directory containing a bunch of ATR files, they show up fine when I do a dir of the hard drive; it only seems to return nothing when I try to list a "hard drive" containing files I wrote using the emulator itself.