No it shouldn't. Just deleteing a book from your iPad should leave it available for download from iTunes again in the future. Once you've bought the book it's yours to download onto as many iOS devices as you like.
Are you sure the book isn't listed under Purchased in iBooks Store? Did you do a search for it? Tap the "All" tab and then type title of book (or part thereof) in the search box at top right of the screen and Search. If you have purchased the book then it should show up in the search results, with the iCloud download icon rather than the price button you get for books in the store you haven't purchased (why it doesn't limit the search to just the titles you have already purchased given that you're in the Purchased section I don't know, but that's the way it works unfortunately.)