I have 7000+ books on my PRS-950. With PRS+ I can access folders on an SD card and there is no slow-down whatsoever. I would think (although I don't actually know) that as long as the chosen ereader can do the same, then all will be well. Personally I have no comprehension as to why anyone would want to do it differently.
In practice that means a reader from Onyx, Pocketbook or Bookeen, so maybe you'd best enquire in those forums and see if there aren't some people who use their just as you've suggested.
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