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I have no issues with books disappearing from iTunes, and I also have a large library on my iPad. It sounds as if you may have one of your iTunes settings wrong for what is required to work correctly with iTunes - have you checked carefully that they are as is specified for working with Calibre?
The greatest frustration is that it does not seem to be possible to control the ordering shown in the iBooks bookshelf from the Calibre end! All new books always appear at the top. However I suspect that is an iBooks issue rather than a Calibre one. IBooks could do with some more ordering options such as support for ordering by author or tags, or folder support. I guess these could come in a future release. I sometimes use Stanza instead on the iPad simply because then I can do over-the-air downloading either via the Calibre Content server or via my calibre2opds generated catalog.
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