I'm having the same problem. IIRC, they are missing a step from the previous directions... Please don't take my word on this, It's been too long, I'll check, and repost.
When you are sshing into the device, you are sshing into the filesystem that you dd'ed onto the sdcard. It's really nothing more than a mockup of the real filesystem. You'll need to mount the actual filesystem in order to get access to the real /mnt/app.
when you finish sshing into the nook,
# cd /dev; mknod mmcblk1p6 b 179 14 ; mount -o rw mmcblk1p6 /mnt
That's if I actually understand what is going on. Which is doubtful. I've been off of linux too long. I can't get #nookcolor to respond to this question either.
Anyone willing to confirm/deny/redicule me?
I'm willing to confirm, as I just tried it, and there's glorious app, mounted at /mnt. Muchos gracias!