Nooks mount as a mass storage device; You drag your files over, disconnect and go into the library - it'll check for new content and that's it, you're done.
Calibre is free and does exactly what you specify; I can write something in plaintext, in notepad, and have Calibre convert it into various formats for me, automatically on a per-device basis; so for device A I might have it auto-export as.epub, and for device B as.pdf and so on and so forth.
You can make a PCI blank with a set of crenellations in; Loop your peripheral cables through said crenellations, padlock your case shut, lock it to the desk and you're good.
You can also buy expansion blanks with the crenellations already in, but you've probably got a load laying about anyway....