I just read this thread, and I'm quite surprised by all the comments about the kindle. Just so you know, whilst it doesn't support a tiered directory structure, once you have uploaded PDFs, you can assign them to one or more collections.
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Its very similar to the label system in google, albeit only at one level. Doesn't that go a long way to dealing with the need, or am i missing something?
The problem is the "once you have uploaded" bit. What you really want in such a device is the ability to transfer the current set of plates efficiently. You don't want to have to check what has changed and then upload the changed plates -- that's almost as painful as using paper. That means that the structure has to transfer to the device with the files -- unless you want to organise them into collections afresh every update.
EuroFPL came up with a sensible compromise -- its plates are grouped into files by airport and each PDF file has an index, also available as a .pdr Kindle index.