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True, iBooks converts the .epub file names to some "strange" character sequence. I don't know if Apple has publicly documented this but, assuming the mapping function is known, calibre can simply implement the same mapping function.
I personally don't care if calibre knows what I have on my iPad. I just look on my iPad to see what I've got there, and if I want something additional I just click-drag it from calibre to iBooks. When I don't need a book on my iPad anymore, I just delete it in iBooks and sync with the iPad without doing anything in calibre. calibre still manages my master collection of books, and I haven't seen the need for calibre to know what's actually on the iPad.
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